Rhynchocypris oxycephalus and Barbatula toni were not present in the Chishui River before. However, in recent years, both two species has be found in the Baisha River, a tributary of the Chishui River. Therefore, their sources and future survival possibilities should be paying more attention. We analyed their morphological characters and mitochondrial Cyt b gene sequences tracing where the two fish species R. oxycephalus and B. toni came from and built the ecological model to predict their ecological adaptability in the Chishui River. We got the the following results: 1) the individual size between wild and cultivated population was significantly different; 2) three morphological characters got from the cultivated population are higher than those of the wild population. Based on Bayesian inferences, maximum likelihood and neighbor-joining methods for all haplotypes, phylogenetic analyses revealed that samples of R. oxycephalus from Chishui River including both cultivated and wild individuals firstly clustered with samples from Yangyun population Liaoning province, Northeast China (Fig. 2); samples of B. toni from Chishui River firstly clustered with those from Inner Mongolia, Liaoning and Hebei province (Fig. 3). Moreover, the results from the ecological niche model, MaxEnt, showed that the Baisha River, a tributary of the Chishui River, has a moderately suitable area for R. oxycephalus (the suitability probability was 0.620, Fig. 4), while the suitability probability for B. toni in this area was rather low (the suitability probability was 0.025), which with probably due to the little distribution information of this species (Fig. 4). The water temperature at the sampling site was relatively low, which was close to the water temperature of the northern sampling sites. It could be inferred that this area has suitable conditions for the survival of R. oxycephalus and B. toni. To sum up, these two exotic species in the Chishui River were from the northeastern of China, and adapted well to the local environment. This result was consistent with the survey of the local farmer. In the future, population monitoring needs to be strengthened to prevent them becoming invasive species.