The heredity of autogeny in Culex pipiens from northern coast, Alexandria, Egypt, was investigated. Parental females laid more autogenous egg rafts than F1, F3, and F4 females. No significant difference was found in the autogeny rate when F3 female mosquitoes from an autogenous colony mated with males either from an autogenous or anautogenous colony. Similarly, when F3 males from an autogenous colony mated with females either from an autogenous or anautogenous colony, statistically comparable autogeny rates were recorded. However, when females from an anautogenous colony were allowed to mate with males from an autogenous colony, the autogeny rate was statistically higher than that when females from an autogenous colony mated with males from an anautogenous colony. Molecular analysis using ISSR was suitable for detecting polymorphic banding patterns between autogenous and anautogenous specimens of mosquitoes. The ISSR technique succeeded in showing 13 different molecular markers which can be relied upon in distinguishing between populations. Molecular distances among populations were low, ranging between 0.114 and 0.284. On the other hand, cluster and principal coordinate analyses showed that anautogenous specimens were contiguous in one group and separate from autogenous specimens. The ISSR technique is therefore able to detect genetic differentiation among the studied populations, and to distinguish between autogenous and anautogenous mosquitoes from the northern coast of Egypt.