Island species, particularly endemics, tend to have lower genetic diversity than their continental counterparts. The low genetic variability of endemic species and small populations has a direct impact on the evolutionary potential of those organisms to cope with changing environments. We studied the genetic population structure and morphological differentiation among island populations of the Galapagos Dove (Zenaida galapagoensis). Doves were sampled from five islands: Santa Fe, Santiago, Genovesa, Española, and Santa Cruz. Five microsatellite markers were used to determine genetic diversity, population structure, gene flow, and effective population sizes. F_ST and R_ST values did not differ among populations; in general, populations with greater geographical separation were not more genetically distinct than those closer to one another, and estimated gene flow was high. There were no significant differences in allelic richness and gene diversity among populations. Although there was extensive morphological overlap among individuals from different island populations for both males and females, we found significant differences in overall body size only between populations on Santa Fe and Santa Cruz (males and females) and between Española and Santa Fe (males only). Significant differences in body size between populations undergoing high rates of gene flow indicate that differentiation may be due to either phenotypic plasticity or ecotypic differentiation. Based on the results of previously conducted disease surveys, we discuss the conservation implications for the Galapagos Dove and other endemics of the archipelago; we also discuss the possible effects of wind currents on gene flow.