【Objective】 In order to understand the current situation of wild resources for three Cranoglanis populations and to evaluate the species validities of three species.【Method】The genetic structure and genetic variation of three Cranoglanis populations (C. multiradiatus, C. bouderius and C. henrici) were investigated by sequencing the Dloop genes in the mitochondrial control region. 【Result】Among 84 individuals from the three populations, fourty-three hapotypes were detected, indicating a relatively high haplotype diversity and low nucleotide diversity. The lowest hapotype diversity (Hd) and nucleotide diversity (Pi) were both found in C. multiradiatus group(Hd=0.871, Pi=0.006 4). Tajima’s D neutral test and nucleotide mismatch distribution analysis showed that the three populations were getting stable without experincing any large-scale expansion. Fst analysis suggested that C. multiradiatus had certain genetic differentiation compared to C. bouderius and C. henrici, while the latter two did not have any obvious differentiation from each other. The genetic distance between C. bouderius and C. henrici was 0.000. 【Conclusion】The wild resources for Cranoglanis are relatively poor and the case in C. multiradiatus is the most serious. C. bouderius and C. henrici are considered to be one subspecies, as well as C. multiradiatus being another subspecies of Cranoglanis.