Bokermmanohyla saxicola is endemic to the Espinhaço Mountain Range (southeastern Brazil), and broadly distributed in montane meadows of the Serra do Cipó. Four microsatellite regions were located through genomic library screening for this frog, two of which were chosen for population structure analyses given their high variability levels (10–11 alleles assayed in 75 tadpoles from five different streams). Overall F_st was 0.056, and the studied demes fitted isolation by distance model expectations, but the increase of F_st values was unrelated to increases in geographic distance, as it would be expected in drift-gene flow equilibrium conditions. Microsatellite markers revealed lack of pairwise genetic differentiation in spatially close demes and also in some distant ones, a pattern that may be caused by the combination of limited migration ability and past event effects contingent upon suitable habitat conditions for frog movement.