they are, in many many ways, similar. Both are (mostly) diurnal, have the same toe and foot structure, have the same build, dietary needs, range, etc. But the main difference, i believe, is in genetics and bone structures. As you may have noticed, lygodactylus are generally much smaller than phelsuma, which is one of the main differences. I have often wondered what exactly defines the two genuses, but i suppose it is just one of the taxonomic fiddly bits.
I'm sure somewhere on the web you will be able to find a bit more detail. Even my in-depth Madagascar Natural History book doesn't go into detail defining the two. appearance-wise they are generally very different (colouration), though a few are more mottled and would appear to be closely (to the eye) related to lygodactlyus.
i hope this helps, but do more research if you are more curious