The greater flamingo Phoenicopterus roseus is a long-lived colonial waterbird species, characterized by a large range encompassing three continents, a very limited number of breeding sites, and high dispersal abilities. We investigated both the phylogeographic history and the contemporary extent of genetic differentiation between eight different Mediterranean breeding colonies of greater flamingos sampled between 1995 and 2009, using both mitochondrial DNA and microsatellite markers. We found no significant differences in allelic richness or private allelic richness in relation to colony size. Overall, no genetic population differentiation was detected using either mitochondrial or microsatellite markers. F-statistics and Bayesian clustering methods did not support any significant genetic structure. Analysis of both mitochondrial DNA and microsatellites indicated that populations have undergone a bottleneck followed by rapid growth and expansion. The average time since expansion was estimated to be 696 421 yr (90% CI: 526 316–1 131 579 yr). We discuss our results in relation to both the possible historical events accounting for the present genetic structure and relevance to conservation and management of the species.