Culex pipiens sensu lato mosquitoes were collected from 24 gravid traps (mid-June to mid-October, 2005) in Fresno County, CA. Captured gravid females were allowed to oviposit before sibling species identification by Ace.2 PCR and detection of West Nile virus (WNV) RNA by RT-PCR were performed on the mother and her offspring. Of the 442 Cx. pipiens s.l. female mosquitoes collected, 88 were positive for WNV viral RNA (peaked in August) with no significant differences among complex members or habitat. Vertical transmission was detected in 4 out of 20 families originating from WNV-positive mothers, however, in only a small number of offspring from each family. Out of 101 families that had PCR-based maternal and offspring identifications, the offspring from 15 families produced inexplicable amplicon patterns, suggesting ambiguities in the PCR assay identifications. Male genitalia (DV/D ratio) and Ace.2 PCR identifications revealed numerous discrepancies in our ability to accurately determine the identity of Cx. pipiens complex members in the hybrid zone of Fresno County.