Previous work on the distribution of historecognition alleles in botrylloid ascidians has revealed extensive polymorphism at this locus, but has yielded little information on the distribution of alleles among populations and the rate of allele proliferation within populations. We first present preliminary data on the genetics of historecognition in Botrylloides diegense, a West Coast native that was introduced to the East Coast in 1972. We then compare the distribution of alleles in 2 populations of different size in a Maine estuary. Finally, we compare the alleles in those 2 populations to the alleles in a population at Woods Hole, the site of the original introduction. Our results indicate that a small, peripheral population contains fewer alleles than a large population and suggest that alleles have proliferated rapidly since this species was introduced to the East Coast. The rapid proliferation of alleles reported here provides additional support for the hypothesis that historecognition systems are subject to frequency dependent selection in natural populations. © 1992 Wiley-Liss, Inc.