When you work with fish, www.fishbase.org (or one of its mirror sites) is a great resource for questions like this. According to fishbase, G. affinis has more scales on the lateral line (32-33 as opposed to 28-30 in G. holbrooki), as well as lacking spines in the dorsal and anal fins (G. holbrooki has one) -- see http://www.fishbase.se/summary/Gambusia-affinis.html and http://www.fishbase.se/summary/Gambusia-holbrooki.html

I agree that counting scales is a possibility to get a general idea, but different authors have different and even overlapping numbers for each species rangin from 26-34. Aditionally the dimorphisms among gender and the problem of missing anal / dorsal spines in G. affinis makes it rather difficult.

I have to mention that I prefered it when it was just Gambusia affinis holbrooki.

Are there data on the genetic difference between these 2 species? 

The 'classical' revision of the Poeciliidae is still useful for distinguishing between Gambusia affinis and G. holbrooki (there treated as subspecies):

Rosen, D. E. and R. M. Bailey 1963. The poeciliid fishes (Cyprinodontiformes), their structure, zoogeography, and systematics. Bulletin of the American Museum of Natural History v. 126 (art. 1): 1-176.

Rosen & Bailey (1963: 95) remarked the following:

They are distinct in gonopodial characters; holbrooki has a series of prominent denticles on the posterior surface of ray 3 and a rather short, unsegmented bony claw on 4p, whereas affinis lacks the denticles and has a longer, segmented claw. The dorsal rays characteristically number seven in holbrooki, six in affinis.

The paper is available online under the link:

http://digitallibrary.amnh.org/handle/2246/1123

For further information on references and current status of the species you may wish to consult the Catalog of Fishes online:

http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp

The best way to clearly distinguish G.affinus and G. holbrooki is with gonopodal characters as Ronald Fricke suggests. You may also look at Mary Rauchenberger's revision of Gambusia: American Museum Novitates 2951. This work is available online. There are detailed diagrams of the relevant gonopodial characters shich I have found extremely useful.