The Klamath-Siskiyou ecoregion of northern California is one of the most diverse temperate coniferous forests. A network of “late successional reserves” (LSRs) has been established to maintain characteristics of late successional forest and to promote late successional characteristics in younger stands. Also, an important goal of conservation management is the maintenance of genetic diversity of ecologically important species. However, this management strategy has not yet been implemented among the LSRs. This study examined the level of genetic diversity among populations of a soil-inhabiting beetle, Acrotrichis xanthocera (Matthews) (Ptiliidae), within the LSR network. Using a partial DNA sequence of the mitochondrial cytochrome oxidase I gene, a total of 31 haplotypes were identified for 117 individuals. Genetic fixation indices and phylogenetic and nested clade analyses all suggest moderate gene flow among five LSR and five non-LSR populations. In addition, haplotype diversity was high and the occurrence of unique haplotypes was common for most populations, which suggests current or past isolation of some populations. These results suggest the LSR network maintains considerable genetic variation for this beetle. However, the genetic variation was not equally distributed among the LSRs. Thus, to facilitate gene flow throughout the ecoregion, it is suggested that future LSRs should reduce gaps among the current LSRs.