Microsatellite and mitochondrial DNA (mtDNA) variability data were used to study outbreaks of Mediterranean fruit fly in California in the years 1992–94 and 1997–99. A total of 359 flies caught in monitoring traps during these years were examined at three polymorphic mtDNA restriction sites and two microsatellite loci. Composite genotypes obtained through analysis of these markers indicate at least five independent introductions of medflies into California between 1992 and 1998. Whereas the majority of specimens displayed a single mtDNA haplotype (AAA), variation of microsatellite alleles among these flies suggests at least one additional introduction in 1993 into southern California. Flies displaying the AAB haplotype sampled in 1992 both in northern and southern California shared microsatellite alleles absent in AAA flies although lacking others commonly found in AAA specimens, thus supporting the hypothesis of an independent introduction of these flies from a different source. In contrast to earlier infestations, a few specimens caught in southern California in 1993 and again in 1998 showed both mtDNA and microsatellite patterns consistent with a Hawaiian origin. Single flies collected in Santa Clara County in 1997 and in El Monte, Los Angeles County & in 1999 most likely represent a sixth and seventh distinct introduction, respectively.