Hybridization between species is likely to be associated with a new ecological impact. However, in termites, reports of hybridization mostly focus on hybrid zones caused by species invasion or the development of initial-stage colonies. In this study, we combined microsatellite genotyping with mitochondrial DNA sequencing to investigate the hybridization and adaptive introgression between two sympatric, long-differentiated related termite species, Reticulitermes flaviceps and R. chinensis, in nature. Similar levels of mitochondrial and nuclear genetic diversity were found in R. flaviceps and R. chinensis. Asymmetric interspecific genetic differentiation was observed between mitochondrial and nuclear genes, with high genetic divergence found in mitochondrial DNA but low genetic divergence in nuclear genes. Our results indicated a lack of mitochondrial gene exchange in R. flaviceps and R. chinensis but unconstrained nuclear introgression between them. This asymmetric genetic differentiation between nuclear and cytoplasmic material strongly suggests that there is interspecific hybridization between R. flaviceps and R. chinensis in nature, which provides new insight into the dynamics of hybridization and its potential consequences for speciation in termites.