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For a snapshot assessment of the genetic diversity present within Melipona subnitida, an endemic stingless bee distributed in the semi-arid region of northeastern Brazil, populations separated by over 1,000 km distance were analyzed by ISSR genotyping. This is a prerequisite for the establishment of efficient management and conservation practices. From 21 ISSR primers tested, only nine revealed consistent and polymorphic bands (loci). PCR reactions resulted in 165 loci, of which 92 were polymorphic (57.5%). Both Phi(ST) (ARLEQUIN) and theta(B) (HICKORY) presented high values of similar magnitude (0.34, p<0.0001 and 0.33, p<0.0001, respectively), showing that these two groups were highly structured. The dendrogram obtained by the cluster analysis and the scatter-plot of the PCoA corroborate with the data presented by the AMOVA and theta(B) tests. Clear evidence of subdivision among sampling sites was also observed by the Bayesian grouping model analysis (STRUCTURE) of the ISSR data. It is clear from this study that conservation strategies should take into account the heterogeneity of these two separate populations, and address actions towards their sustainability by integrating our findings with ecological tools.