Culex pipiens sensu lato populations represent significant nuisance pests and vectors of West Nile virus in California. Despite multiple years of investigation, identifying, controlling and understanding the behaviors and associated “biologies” of the complex members still remain a challenge. Population structure cluster analysis using microsatellite markers revealed extensive population structuring, particularly in the central parts of the State, over and above what can be explained by the presence of Cx. pipiens, Cx. quinquefasciatus and their hybrids. Ace 2 gene sequencing provided evidence for the presence of Cx. p. molestus in multiple locations both above and below ground in California. Lack of congruence of male genitalia morphology (dorsal and ventral arms/dorsal arm of phalosome) and polymerase chain reaction diagnostic assay identifications coupled with considerable heterozygosity of pyrethroid resistance in time and space all suggest complex population structuring not adequately explained using current concepts.