Microsatellite markers were developed for the fiddler crab Uca mjoebergi for use in paternity assignment. Five highly variable loci were found to amplify reliably in U. mjoebergi, although one locus exhibited evidence for the presence of null alleles, and two loci exhibited evidence of linkage. The number of alleles, expected heterozygosity and probability of paternity exclusion (P > 0.999) suggest that these markers when combined provide sufficient power to determine paternity by exclusion in this species. Three primer pairs were found to also amplify PCR products from three additional fiddler crab species (U. dampieri, U. flammula and U. seismella), and will prove useful for phylogeography and behavioural ecology of fiddler crabs.