Urban colonization by wildlife involves a combination of several different mechanisms, including phenotype or genotype sorting, phenotypic plasticity and microevolutionary adaptation. Combination of these processes can produce a rapid phenotypic, but also genetic divergence of urban versus rural populations. Here, we examined the pattern of genetic differentiation between urban and rural populations of a colonial migratory bird, the black‐headed gull Chroicocephalus ridibundus. To this end, we sampled ca 170 individuals from six (two urban and four rural) colonies in northern Poland, and genotyped them at ten microsatellite loci. Our analysis provided evidence for negligible genetic divergence of urban and rural colonies, as assessed with fixation index FST and Nei's unbiased genetic distance D (mean pairwise urban‐rural comparisons: FST = 0.003 ± 0.001 [SE] and D = 0.012 ± 0.006 [SE]). Bayesian clustering methods provided support for homogeneous genetic structure across all urban and rural populations. Also, we found no support for reduced allelic diversity in urban versus rural colonies. These results stand in a stark contrast to the previous findings on the genetic consequences of urbanization in birds. We hypothesize that this pattern could possibly be attributed to the important life‐history characters of the black‐headed gull, including coloniality, migratoriness, and high dispersal propensity. Our study provides a novel insight into the urban landscape genetics, underlining large variation in the mechanisms of urban colonization and its genetic consequences in wild animal populations.