RAP1A protein is a small Ras-like GTPase that accumulates during muscle differentiation. In this study, we observed variable intracellular location of the endogenous RAP1A protein and concomitant relocation of the late endocytic compartments in differentiating myogenic cells. By monitoring the nucleotide-bound form of RAP1A protein, we established that the various protein localizations were related to the GTP/GDP-bound state. To carry on our study, we raised stable myogenic cell lines overexpressing wild-type or mutated forms of RAP1A. Myoblasts overexpressing the GTP-bound mutant did not display specific changes of RAP1A and of late endocytic compartments locations. In contrast, the GDP-bound mutant clustered with acidic structures in the perinuclear region of myoblasts. In addition, we observed that overexpression of GDP-bound RAP1A protein induces disturbances in the maturation process of the lysosomal enzyme cathepsin D. Whereas ectopic expression of wild-type or GTP-bound RAP1A proteins inhibited myogenic differentiation, the GDP-bound mutant favors myotubes formation. From our results, we propose that RAP1A protein may regulate the morphological organization of the late endocytic compartments and therefore affect the intracellular degradations occurring during myogenic differentiation.