This study was carried out to determine the effect of genotype, used as a treatment on fertility, hatchability and embryonic mortality of FUNAAB Alpha indigenous chicken. During the cause of the project, a total of 100 birds commercial lines of FUNAAB Alpha of the Genotypes that includes, Naked Neck, Frizzle, Normal feather maintained at the Pearl unit at the directorates of university farms and adequate feeding and water were administered to the birds all through the period of the project. Semen was obtained from sires using a standard procedure and inseminated into the dam to produce fertile eggs. Eggs were collected, labelled according to genotype and then transported to the hatchery unit where it was stored at a very low temperature, to retain the content inside the eggs. Eggs are set on weekly basis into the incubator, candling was carried out at the 18th day after setting the eggs, to identify fertile eggs. All contaminated, bangers and infertile eggs were discarded while the fertile eggs were set back into the incubator. All hatched eggs developed into chicks on the 21st day and all dead-in-shell and weak-in-shell were set aside and the estimated values for them were noted. At the end of the research, it was noted that all the genotype used in the cause of this project had significant effect on the percentage fertility and percentage dead-in-shell. However, percentage hatchability, percentage dead-in-germ and percentage weak-in-shell had no significant effect on all the genotype used in the cause of this project. This depicts that, genotype has a great influence on estimated hatchability and Dead-in-shell of the eggs, resulting in embryonic mortality of eggs. Dead-in-shell is higher in naked neck genotype, followed by normal feather and least in frizzle while weak-in-shell is high in normal feather, followed by naked neck and least in frizzle.