In the current study, two euglossine species, Exaerete smaragdina and Eulaema nigrita, a cleptoparasite bee and its host, respectively, were used as models to: (i) access the genetic diversity and population structure of both species, sampled along a wide latitudinal range of Atlantic Forest, where the distribution of El. nigrita and Ex. smaragdina co-occurs; (ii) investigate the evolutionary history of these species through the Atlantic Forest, and in a wider scenario, to examine the evolutionary history of these species across others forest domains. Analyses involved males of El. nigrita and Ex. smaragdina sampled through Brazilian territory, including 19 sites in the Atlantic Forest. Bayesian Skyline Plot (BSP) was used to infer possible climate oscillations on population of both species over time. The BSP revealed stability in effective population size for both species in most of the Plio-Pleistocene period. However, BSP results aligned to the starlike configuration in the haplotype network, neutrality test, and population diversity patterns indicated population expansion of the two species during the late Pleistocene. Our findings suggest areas of potential refugia to the climatic oscillations of the Pleistocene in the Atlantic Forest in the Brazilian states of Espírito Santo for El. nigrita and Pernambuco for Ex. smaragdina.