Genera is a plural noun; it's used as the plural of the singular genus. Since any single species only belongs to one genus, the sentence you quote ("It is best not to keep [it] with fish of the same genera") doesn't seem to use proper grammar. "It is best not to keep it with fish of the same genus" would be correct.
If some plural noun referring to a family of fish, or some larger category of fish, were used in place of "it", I think the sentence might be acceptable. Something like "It is best not to keep acanthurids with fish of the same genera" or a general statement like "It is best not to keep certain species of fish with fish of the same genera". Even though this structure doesn't seem incorrect, it still seems more awkward to me than the structure with a singular noun phrase after "keep" and a singular "genus" after "same". I guess the way I would try to evaluate it is by replacing the word "genera" with some word that takes a regular plural like "families": if the situation was that the fish were aggressive to other fish that belonged to the same families, what kinds of sentences would sound natural?
- "When dealing with members of the order Perciformes, keep them away from others of the same families."
- "It is best not to keep perciforms with fish of the same families."
- "It is best not to keep certain species of fish with fish of the same families."
I think these sentences are technically correct because they have consistent pluralization but "of the same families" does sound a bit odd to my ears even so. Probably, sentences of this structure with plural noun phrases are not as common as sentences of this structure with singular noun phrases.