Recent discussion of genetic benefits of polyandry and female mate choice has distinguished between two potential factors influencing offspring quality: (i) some males carry higher quality genes and (ii) males and females differ in their degree of genetic compatibility. We examined evidence for effects of good genes and genetic compatibility on embryonic survival of sea lamprey (Petromyzon marinus), a fish species with external fertilization that spawns in North Atlantic rivers. Using in vitro fertilization, we made all possible crosses among 10 males and 5 females collected in the spawning grounds. Male identity did not have any significant effect on hatching success. However, female identity and male x female interactions had a highly significant effect on hatching success. Our results suggest that genetic compatibility between male and female genomes plays an important role in embryo survival during the early stages of development in the sea lamprey.