Objective] To analyze the sequence difference of the SSU rDNA variable regions of Leishmania isolates from hilly foci and plain foci of China. [Methods] Specific SSU rDNA fragments from nuclear DNA of five Leishmania species and isolates were amplified by PCR. The amplified DNA fragments were cloned into pGEM R-T Easy vector. The specific fragments were sequenced by the automated DNA sequencer. [Results] Sequence analysis showed that the amplified DNA fragments of five Leishmania species and isolates were all 392 bp in length, point mutations were located in the two unique sequence (UQ-Ⅰ and UQ-Ⅱ); L.d.SC10 and L.d.GS7 had two same point mutations in UQ-Ⅱ, only L.d.GS7 had one in UQ-Ⅰ; no insertion/deletion. [Conclusion] Sequence difference of the SSU rDNA variable region existed between Leishmania isolates from hilly foci and plain foci; The sequences of the SSU rDNA variable regions of L.d. SD2 isolate and L.infantum were identical.