Combined analyses of mitochondrial DNA (mtDNA) and microsatellite loci were performed to assess the genetic differentiation of two spring-spawning ciscoes from each other and from sympatric Coregonus albula in two German lakes. Polymorphism was screened at six microsatellite loci and mtDNA for a total of 247 and 94 ciscoes, respectively. Microsatellite data showed a weak differentiation between spring-spawning Coregonus fontanae and sympatric C. albula in Lake Stechlin (FST = 0–0·008), whereas a significant differentiation was observed between spring-spawning Coregonus lucinensis and sympatric C. albula in Lake Breiter Luzin (FST = 0·013–0·039). A more pronounced genetic difference was observed between both spring-spawning species (FST = 0·05–0·128). Shared mtDNA haplotypes among sympatric species within both Lake Stechlin and Lake Breiter Luzin were observed, whereas no haplotype was shared between C. fontanae and C. lucinensis. These results suggest an independent origin for spring-spawning ciscoes in each lake. Evidence is also provided for mtDNA introgression of Coregonus sardinella into C. lucinensis and C. albula in Lake Breiter Luzin. Postglacially, this species or at least a population which showed mtDNA introgression has colonized the Baltic Sea basin up to the glacial margin that was located between Lakes Stechlin and Breiter Luzin.