In the early 1970s, incidental catches of lobster around Masirah Island had established the lobster fishery in Oman, which then expanded rapidly developing into a large commercial fishery. Currently, this lobster fishery is suffering overexploitation as seen from the long-term decline in landing. Hence a serious effort toward a sustainable fishery management of the species is crucial. A successful fishery management regime requires understanding the population genetic structure, which will better clarify population connectivity and stock structure. The attractive features of Microsatellites enhance their successful application in a wide range of fundamental fields including genetic mapping, population structure, and evolutionary processes. They are considered as one of the few molecular markers that provide answers to fine-scale ecological issues. In this study, 49 novel microsatellite loci consisting of perfect di-, tri-, tetra- and penta-nucleotide repeats have been developed for Panulirus homarus using a cross species primer amplification strategy based on Panulirus ornatus "Roche 454" shotgun generated sequencing. Microsatellites were efficiently co-amplified in 14 multiplexes, resulting in consistent and easily interpretable genotypes. Multiplexes were tested in population genetic analysis of P. homarus from three locations in Al Wusta governorate at the Arabian Sea coastline. Six loci were monomorphic. The remaining 43 polymorphic microsatellite loci were highly informative in terms of Polymorphic Information Content (PIC), Allelic Richness (Ar) and Gene Diversity (GD) with mean values of 0.56, 5.7 and 0.55 respectively. The number of alleles per locus ranged from 2 to 22 with the observed (Ho) and expected heterozygosity (He) ranging between (0 - 0.947) and (0.049 - 0.937), respectively. A significant deviation from Hardy-Weinberg equilibrium was observed in 23 loci, probably due to presence of null alleles, homozygote excess or deficit. The percentage of significant pairwise Linkage disequilibrium was 8.5% of the total tests. The high success in primer cross-species amplification of these microsatellite markers indicates their utility for genetic studies of different Panulirus species. Genetic diversity was similar in the three sampling locations representing absence of barriers to gene flow. Estimates of genetic differentiation by Analysis of Molecular Variance (AMOVA) indicated absence of population structure (Fst: 0.01, p-value: 0.97) as supported by low and non-significant pairwise For values (0.007 -0.016) and the high levels of gene flow between sampling locations (0.39 -0.91). While the new model based-clustering methods indicated presence of three genetic clusters, however they are not geographically restricted. Besides, two main phylogenetic clades contained admixtures of individuals. From these results and in terms of fishery management, P. homarus in Al Wusta coast should be treated as one single admixed stock.