Aedes albifasciatus is a floodwater mosquito widely distributed in Argentina. It is important from economic and medical points of view. A 4-year survey of seasonal variation in allele frequencies in a population of this species was undertaken to determine possible changes in the genetic structure and their correlation with environmental conditions. Significant temporal variation was detected at most of the loci, but it did not follow a cyclic or seasonal pattern. Multivariate analysis of principal components showed a remarkable homogeneity of samples collected from December 1993 to April 1995 and a clear differentiation of the November 1991, March 1992, and November 1993 samples. This variation could be correlated with the magnitude of rainfall occurring in the area. Passive transport of larvae by water streams and river freshets produced by floods would have mixed larvae from breeding sites with different allele frequencies, causing the genetic differentiation observed.