When you buy a pair of Apistogramma from a LFS...

[Don90]

Will the male be somewhat related to the female?

If you breed them, would it be considered inbreeding?

[genes]

There is a possibility that they are related. Or that they have been used for many generations of inbreeding. So look out for deformities like finnage, body posture etc.

If you have cash to spare, you can always buy the wild caughts when they are available. However, these guys will cost you a premium. Usually costing around the hundred to thousands depending on the species. Another alternative is to source from hobbyist their F1 or F2 fries. F1's are the fries from the wild caught parents. And F2 the fries from the F1.

Quality of F2 is still not too bad. However, to breed them will still be considered inbreeding. My experience with breeding is that with a wild caught pair, there are more fries that holds good finnage and colouration. As you continue breeding from the fries, you will still get fries with good finnage and colouration, but the number of them reduces as you inbreed.