The Tsetse fly. Glossina palltdipes. (Diptera: Glossinidae) is an important vector of animal trypanosomiasis It has also been implicated in the transmission of pathogens that cause human African trypanosomiasis. Understanding how G. palhdipes populations vary temporally is necessary for effective intervention. Temporal variation in allele frequencies at eight microsatelhte loci was assessed by sampling local populations of G. palltdtpes. Samplings were carried out in 2000, 200 I, and 2003 in the Lambwe Valley and Nguruman areas in Kenya. Six polymorphic loci were scored. Allele frequencies were homogenous between seasons. Genetic differentiation was higher among dry season samples (F,, = 0.051, G" = 0.047) than wet season samples (F;r = 0.041, G" = 0.03 7). Differentiation between pooled dry season and pooled wet season samples did not differ (F,r = 0.008, G" = 0.004). Analysis of variance revealed no substantial genetic subdivision in seasons or years. It is concluded that G. pallidipes populations are more aggregated during the dry season, resulting in stronger measures of genetic differentiation when compared with wet seasons. However, season and time had no effect, indicating relative stability of G. pallidipes populations. Thus, strategies for suppression of G. pallidipes in the country should adopt measures that may not reduce effectiveness indifferent times of the year.