A key assumption of many allopatric speciation models is that evolution in peripheral or isolated populations is facilitated by drastic reductions in population size. Population bottlenecks are believed to lead to rapid changes in gene frequencies through genetic drift, to facilitate rapid emergence of novel phenotypes, and to enhance reproductive isolation via genetic revolutions. For such effects to occur, founding populations must be very small, and remain small for some time after founding. This assumption has, however, rarely been tested in nature. One approach is to exploit the polymorphism of the major histocompatibility complex (Mhc) to obtain information about the founding population. Here, we use the Mhc polymorphism to estimate the size of the founding population of Darwin's finches in the Galápagos Archipelago. The results indicate that the population could not have been smaller than 30 individuals.