Penaeid prawns in Ungwana Bay, Kenya, are heavily exploited by artisanal fishers and industrial bottom trawlers. Human activities in mangrove and estuarine areas may affect prawn nursery habitats and influence juvenile recruitment to fished areas, therefore it was important to investigate recruitment patterns in the bay. To test the hypotheses that single genetic stocks exist, we utilised a combination of mtDNA sequence and microsatellite data. Three dominant sympatric species, Penaeus monodon, Fenneropenaeus indicus and Metapenaeus monoceros were targeted. Sample sites were chosen to represent the bulk of fishery activities, and included estuarine juveniles and offshore adults. An exceptionally high mtDNA haplotype diversity, coupled with low nucleotide diversity was observed for all three species and there was no genetic differentiation among sampling sites. Genetic panmixia was confirmed by the microsatellite analyses of P. monodon. Juveniles that recruit to adult populations in Ungwana Bay most likely originate from local estuaries, and conservation of the prawn nursery habitats along the edges of the bay is advocated. Each of the three species represents a single management unit, and the identification of spatial management strategies to mitigate resource-user conflicts should rather consider other ecological and socio-economic factors than the genetic delineation of stocks.