The bark weevil, Pissodes yunnanensis Langor and Zhang, is an important pest of young Yunnan pine, Pinus yunnanensis Franchet (Pinaceae), in southwestern China. Populations of the host and weevil are disjunct, especially in the northwestern part of the range in Yunnan province. To estimate maternal gene flow and examine the genetic structure of Pissodes yunnanensis, we sequenced an 840-bp fragment of the mitochondrial cytochrome c oxidase I (COI) gene in 60 individuals from 7 populations in Yunnan and Guizhou provinces. Percent divergence among populations ranged from 0.001% to 2.1%. Nested clade analysis of 21 haplo types showed evidence of genetic structuring that is inferred to be primarily due to allopatric fragmentation and a low level of gene flow. Analysis of molecular variance also showed significant genetic structuring and restricted gene flow among weevil populations, especially between northwestern and eastern regions of the range. Such genetic structuring may be important for pest management programs. Phylogenetic analyses comparing the same 761-bp sequence among P. yunnanensis, Pissodes punctatus Langor and Zhang from southwestern China, and five Nearctic species of Pissodes showed that (i) the two Chinese species were most closely related to each other, (ii) the four species in the P. strobi (Peck) species group formed a distinct clade, and (iii) these two clades were more similar to each other than to the Nearctic species P. affinis Randall.