We observed the habits of two Eupristina species living in Ficus altissima. Only two fig wasp species, Eupristina altissima and Eupristina sp., are found to be associated with the syconia of Ficus altissima around the Fuzhou area, China. The former wasp is the Ficus altissima pollinator, while the latter wasp does not have pollination behavior. Some subtle differences are found in females of both wasp species regarding body color, antennae, pollen pockets, comb of setae on the fore coax. So far, no clear characters have been found to be used for distinguishing the males of these two wasp species. To better understand the genetic relationship between E. altissima and Eupristina sp., we cloned the mitochondrial Cytb and COI genes derived from both E. altissima and Eupristina sp. collected from five different locations in Fuzhou. Eupristina verticillata, the pollinator of Ficus microcarpa, was used as an outgroup control. We analyzed the base composition and genetic distance of the gene sequences and constructed a neighbor-joining phylogenetic tree to investigate the genetic evolutionary relationships. The data are summarized as follows: (1) The base composition of Cytb and COI show a high adenine (A) and thymine (T) bias (Cytb, A+T=75.3%; COI, A+T=75.5%), which pattern is consistent with the typical characteristics of mitochondrial gene sequences of hymenopteran. (2) Genetic distance analyses of two wasps groups show that the average distance of the Cytb sequence within each group of E. altissima and Eupristina sp. are 0.0092 and 0.0030, respectively, far beyond the average genetic distance between E. altissima and Eupristina sp. that is 0.1588; COI sequence analyses show that the average genetic distances within each group of E. altissima and Eupristina sp. are 0.0065 and 0.0205, respectively, although the average genetic distance between E. altissima and Eupristina sp. is 0.1043. Thus, the genetic distance between the two groups is significantly greater than that found within each respective group. Statistic analyses of the Cytb sequences derived from 6 genera and 34 species of wasps from GenBank show that the interspecies genetic distances of the Cytb sequence are between 0.0811 and 0.1723, and the interspecies genetic distances in the COI sequences derived from 6 genera and 28 species of wasps are between 0.0939 and 0.1986. These data suggest that the genetic distance between E. altissima and Eupristina sp. has reached to an interspecies difference level. Therefore, our molecular marker studies support the morphological characterization, namely E. altissima and Eupristina sp. are indeed two different species. (3) Only a slight difference is found in females between the two species regarding the morphological characteristics, and no tangible difference is found in the males. However, the data of genetic distances derived from Cytb and COI sequence analyses consistently show the significant differences between the two species regardless their genders. It is likely that the morphological differentiation lags behind the genetic differentiation and the female wasps may evolve faster than the male wasps in the phenotypic features. The females fly out from figs after the emergence, which may be significantly affected by environmental factors resulting in the morphological differentiation between the female wasps of the two species. In contrast, the male wasps of the two species live in the closed darkness syconia with constantly environment lifelong, thus, no behavior differentiation may occur along with the extremely slow events of phenotypic mutating. The host specificity of E. altissima and Eupristina sp. is not as stringent as previously assumed. The host switching events may have occurred during the fig-wasps co-evolution process.