Islands have been characterized as natural laboratories because of their distinct and often identifiable role in promoting genetic variation and population differentiation, but they have also been considered evolutionary sinks of biodiversity. Here, we extend classical studies of island biogeography based in the Eastern Mediterranean to compare genetic divergences and population structure among birds in insular and continental populations. We focused on populations of six passerine species (Short-toed Treecreeper, Great Tit, Eurasian Wren, Eurasian Blackbird, Common Chaffinch and Sardinian Warbler) with breeding populations on the islands of Cyprus and Crete and compared those with a continental population from mainland Greece. We sampled 172 individuals from six species and used double-digest RAD sequencing to examine population-level genetic divergence and structure. Population structure analyses using single nucleotide polymorphisms revealed structure between the islands and mainland for all six species, and this was most pronounced in Short-toed Treecreeper, Great Tit and Eurasian Wren. For all species with the exception of the Sardinian Warbler, the populations from the two islands were more differentiated from each other than either was from mainland Greece, reflecting variation in island colonization dynamics. Patterns ranged from pronounced population differentiation among populations, e.g. in Short-toed Treecreeper, where taxonomic revisions are potentially warranted, to others with weak structure among insular and continental populations, such as in Common Chaffinch and Sardinian Warbler. Although some patterns are consistent with increased rates of genetic drift in smaller populations explaining greater differences among the island populations than either insular population has from continental source populations, in others, including in Eurasian Blackbird and Common Chaffinch, higher nucleotide diversity in Cyprus may reflect a demographic pattern of post-glacial north-westward expansion.