Rhinotermitidae (Isoptera) is an economically important termite family globally. The family is not monophyletic, and the relationships among some of its taxa remain confusing. The taxonomic status of some subfamilies is likely questionable because of various morphological characters of the soldiers and imagoes. Twenty species in 10 genera, representing all six subfamilies of Rhinotermitidae were studied herein. Morphological phylogenetic trees based on 65 characters and molecular phylogenetic trees based on mitochondrial COII and 16SrRNA genes were reconstructed. The sequence composition and genetic distance were analyzed. Based on these results, Rhinotermitidae is polyphyletic. In the morphological trees, the family was divided into five clades. Heterotermitinae and Coptotermitinae were grouped into the most apical one of them and constituted the sister group to Termitidae in the Bayesian inference (BI) tree. In the combined molecular tree, Rhinotermitidae was divided into three clades. The position of the clade composing Heterotermitinae and Coptotermitinae was the same as in the morphological BI tree. The nucleotide sequence analyses also showed that the genetic distances between Heterotermitinae or Coptotermitinae with Termitidae might be closer than those between Heterotermitinae or Coptotermitinae with other subfamilies in Rhinotermitidae. It is postulated that the relationship of Heterotermitinae and Coptotermitinae with other subfamilies of Rhinotermitidae is not as close as that indicated in the current taxonomic system. They might be the real representative of the intermediate lineage from lower to higher termites. These findings further suggest that Heterotermitinae and Coptotermitinae should be separated from Rhinotermitidae and be upgraded as a whole to family rank.