Gaulke (1992; attached) used locally available boat paint for individually marking water monitors in the Philippines. But bead-tagging should also work.

I work with iguanas in the Caribbean. My collaborator from San Diego Zoo and I use  colored bead tags (as suggested by Balázs). Check out the link for more information.

http://www.sandiegozoo.org/images/zoo/education/downloads/curr_iguana_andros_beads.jpg

I worked with  méditerranéenne lizards there are small and I used paint for nails and it works specialy in red , good luck

I'd vote for beads as well. Paint has worked well for me too on smaller lizards and for short periods, but, assuming you don't want to be recapturing the monitors, beads are going to last a good deal longer. 

How many individuals are you tagging? If it's only a few individuals then single beads of different colors could be used really facilitating identification from a distance. 

Thanks all for your contribution.

I am a bit confused about using beads because unlike iguanas, Water monitors don't have crests and spines, So it is safe to use beads in them? And also their habitat is  water, So after surgical threading there are more chances of Infection, isnt it? 

And which area i should focus for insertion of beads ? 

If you need a non-invasive marker, I would also recommend nail varnish of different colors. We also used this to paint individual numbers. You might pre-rub the skin area with 50% alcohol to reduce fatty coatings before painting. Give them 30 minutes to dry before release. Of course this is not a good idea for animals that are about to moult!

How long do you need to be able to monitor these individuals? You can use veterinary tissue adhesive to glue the beads on to the animals if this is a short term study, and a harness system (as used in telemetry studies) with identifying marks can be used for longer term work. I think Geoffrey has the most cost-effective solution covered above.

If you need short term tagging, I also think paint or varnish would do the trick (but as Geoffrey told you, mind the moulting). I used this cheap and simple method on Nile monitors and although they are very aquatic monitors, it works well. However: 1/ it would not be reliable over, let's say, one week, but it depends on the paint you would use: can you implement preliminary tests? 2/ Take care of the size of the individuals you want to tag: garish colors may draw the attention of predators to particularly vulnerable young animals you tag.

If you need longer term identification, I think bead-tagging could still be used on V. salvator. The 1st third of the tail has a crest which is big enough to be pierced and to receive the bead. These animals always have scratches, scars and notches on the tail. And the tip of the tail is often missing... I don't think that any needle piercing in the fibrous crest could result in a major risk of infection.

Aleksandra actually they are present in our University campus and i want to check their movements, population, and territory mapping . It will take about an year, So i don't think paint will work.

and Thanks a lot Alexandre Ciliberti ...I think i should consider bead tagging.

Actually, Alexandre, painting numbers on the top of the head and the side of the body using nail varnish worked for many weeks, and as the animals rarely moulted the entire skin at once, the numbers could be renewed during the moulting process. Of course any animals that have unique combinations of marks (such as failing tail tips and notches on the tail, to be used in identification like the notches in dolphin's dorsal fins) may not need marking at all. Really sophisticated is the use of astronomical star-pattern software to identify individual patterns of skin spots in whale sharks - how much does the water monitor vary in such patterns?

Excellent suggestions. Of course the most effective method is the least invasive, however, this may not be practical. I once worked with a species with individual specimens (to the non-herpetologist) looked identical. However, upon close inspection, each individual displayed a distinct set of individual markings on the head scalation. As they were kept in captivity for part of this research, paint markers would not work (as the frequency of sloughing was accelerated) and the barbaric act of toe-clipping was out of the question. Then, I simply took photographs of each individual animal's head and realised that they were quite distinct. Thus, my form of recognising individuals was based solely on colouration. 

We bead marked Galapagos Land Iguanas for long term studies and followed individual animals for many years. I do not think you would have any problem adding beads to the crest of your study animals.

Some suggestions. Use glass beads and choose colors that you can EASILY identify from a distance. Practice laying beads out at a distance and check your identification before you choose your color/number system. Once you start you really can not make color changes.

Most plastic will loose color and deteriorate in sunlight. Find beads which have holes that are close to the same size of your string-thru material buy enough for marking all of your animals to make sure you use the same colors.

We used monofilament fish line and practiced melting, not burning, the ends to create the knot without the melt touching the actual bead, but making it as snug as possible to the skin. It was a 2 person process. We also noted there was a huge difference in melting properties of different lines. We were odd customers in the bead stores and fishing shops since we tested everything before buying our supplies.

With your monitors you do not want the skin to bunch up un-naturally. It really helps to perfect your process on leather or another similar material before you work on live animals. Practice pinching up the skin and inserting the hypodermic needle, then the line and beads, then removing and laying it flat before melting the final side. You want it snug but not tight or too loose to be the most successful.

We marked over 1,300 of all sized iguanas from adults to freshly hatched iguanas very successfully for many years. We noted that in many, if not all cases the initial hole through the skin remained for the lifetime of the iguanas - 25 years and more.

Good luck.  Sometimes what starts as a short term study can morph into something long-term, so do a great job from the very start.

In regards to painting animals. There is a huge variety of paints used to mark animals.

Before you use paints take time to research their chemical properties and remember that mammals and reptiles can have different reactions to chemicals in those paints.

A rule of thumb,if you do not feel comfortable painting a similar ratio of skin on your body with the paint you place on your study animals, then do not use it on them. Fingernail polishes and paints can still contain chemicals which can cause cancer in humans, or are toxic to the central nervous system, cause birth defects and on and on. While human toxicity studies test mammals, very little is known on the effects to reptiles and amphibians. No study - does not necessarily mean - no harm done.

It is easy to put study animals at risk and directly skew the results perhaps not even knowing the harm that has been done. Be a responsible researcher and cause no harm. I do realize marking is necessary. But give deep thought and research what you put on the skin of your study animals, their lives and genetic contributions to the future may depend on it, even if it is JUST PAINT.

Whatever you do don't paint their heads! Attaching anything to the animal is going to snag, drop off or hinder growth eventually. Recognising pattern on monitor lizards is very tricky because they are often covered in dirt, shedding skin, in the shade etc. It looks easy when they are wet and freshly shed but it's not a practical way of doing it. By far the most efficient way I have found for biawaks is to cut a unique set of notches into the tail crest with a very sharp sterile blade. If it's done carefully they can be made deep enough to be permanent without hurting the animal (you can tell very easily when a biawak is hurt by its reaction). Never cut beyond the crest! These pictures show tail notches made 1-3 years previously. Mid third of the tail is best because the crest is high and they are very unlikely to lose that much tail. Sorry for late reply.

Monitors are clever animals that WILL find a way to remove anything placed on their body. Some burrow, such as V. exanthematicus, and will quickly remove anything you place on their bodies. Toe removal is barbaric, and the varanid is likely to take a bigger chunk out of you! Fortunately, monitors have very distinct heads that vary widely between individuals. We could easily modify facial recognition software to recognize and distinguish between individuals. Any programmers handy?