Would it be possible to rig a spray bar with multiple spray heads that the elephants would walk under? Somewhere that they normally follow each other in roughly single file? If you could do that you could spray them with some type of paint or dye that would not harm them but mark each of them in the herd. A spray rig of this type should not be expensive to build and would be useable in different locations. You could activate it either from motion or remotely or from a blind nearby. 

My other suggest would be paintballs via a paintball rifle or pistol but that would probably hurt a bit when you hit them with it and I don't imagine they would be happy about it. I know it hurts to be hit on our bare skin by a paintball but maybe their skin is thick enough that they would not notice it much. They are air powered and do not make much of a sound. You could be more selective that way about where on the body you marked them.  You would probably need to be careful that they don't see you with the rifle since many of them have probably experienced hunting pressure at some point in their long life. A blind of some sort on top of a vehicle would give you a good vantage point to shoot from and the needed cover to avoid detection.

Just some ideas. 

thanks a lot, oil-based paintball is great, even it has 4-6 years duration !! 

Might not be really practical, but you could fill some water balloons (the ones that burst really easily) with different coloured paints and if there was a hide/tree where you could encourage them to pass by/under you could drop the balloons on the backs of the elephants.  Of course, paint can wash off and you would have to get quite close to individuals, which might not be safe, especially if they get spooked!

I agree with Salindra. I understand that ear characteristics, such as tears, ear venation, and tusk size and shape have been used to identify individual elephants (see Whitehouse & Kerley 2002. Oryx 36, 243–248, and also the associated PhD thesis). I would be doubtful whether paint would be useful for a long term study. Elephants will scratch and rub themselves against trees, alongside wallowing and washing behaviours, I can't imagine the paint lasting long. Also, if a semi-permanent paint is found, there are some ethical questions about whether we should be marking animals with unnatural colours for long periods.

Article Retrospective assessment of long-term conservation managemen...

it's sure we can identify individual elephant by physical characters, but only reseachers, so anyone who meet the color of elephant could  give me lots of information ahout its movement.  

which part of boby for marking is real question

I would think that on the flank either side would be a good location. Definitely enough muscle that how ever you apply the colorant the animal will not feel it or pay attention to it. But also a body part that is big enough to mark well.  Also not a threatening part of the animal so people observing it will likely remember the coloration and not just tusks or eyes. If you mark it to far up like on the back then people on the ground are possibly not going to see the marking.