\textit{Nasutitermes} is the dominant genus in the Atlantic Forest biome, which is one of the five hotspots with the highest number of endemic species and one of the most degraded. Phylogeographic studies reveal historical events that influenced the dispersion pattern of species into biomes, being possible to detect areas of endemism. Thus, this work aims to perform a phylogeographic analysis of the \textit{Nasutitermes jaraguae}, which occurs throughout the Atlantic Domain. We used 34 sequences of the mitochondrial gene COII from the states of Paraíba, Minas Gerais, São Paulo, Espírito Santo, Paraná, Santa Catarina and Rio Grande do Sul. The overall genetic distance among the specimens was 0.014. The Analysis of Molecular Variance revealed significant fixation indexes, indicating a large genetic structure among the colonies (F_{ST}: 0.68110; 0.00000±0.00000), populations (colonies grouped by state) (F_{SC}: 0.53409; 0.00000±0.00000) and groups (populations grouped by region) (F_{CT}: 0.31554; 0.04008±0.00569). In the pairwise analyses, significant values of F_{ST} were obtained among almost all populations (0.37255 to 0.88538). Paraná population did not present significant values, however only one sample has been analyzed so far. São Paulo populations are similar to populations from Santa Catarina and João Pessoa, indicating haplotype sharing or origin by the same ancestral haplotype. Thus, the genetic differences are not exclusively related to geographical distance, but may be associated with the dispersion routes or vicariance events. The hypotheses associated with the current genetic pattern of distribution will be better investigated with the inclusion of the intermediate places. Funding: CNPq (140534/2014-8), FAPESP (2013/20068-9).