Population genetic structure was studied in paddyfield warblers Acrocephalus agricola breeding in NE Bulgaria, SE Russia and S Kazakhstan. We were particularly interested in the degree of genetic differentiation and gene flow of the Bulgarian population due to its geographical isolation, recent origin and unique migratory strategy. Analyses of mitochondrial DNA (mtDNA) showed that there was no divergence between Bulgarian and Russian populations (F-ST = 0.007), whereas those in Kazakhstan differed significantly from the European breeding populations (Russia: F-ST = 0.058; Bulgaria: F-ST = 0.114). The degree of differentiation between populations at nuclear markers (five microsatellite loci; F-ST approximate to 0) was weaker than for mtDNA. We suggest that this relatively weak differentiation over the range of this species reflects a recent postglacial expansion, and results from mismatch distribution analyses and Fu's F-S tests are in agreement. Preservation of small and geographically isolated populations which may contain individuals with unique adaptive traits, such as the studied Bulgarian population of paddyfield warbler, is valuable for the long-term conservation of expanding migratory bird species [Current Zoology 57 (1): 63-71, 2011].