Bamboo borer larvae have caused major losses of bamboo cover in natural forests and plantations. Lack of information on the fauna of bamboo trees has been cited as the contributing factor to poor management of bamboo stands. Genetic diversity information helps understand the effects of different fauna in guiding management plans. Genetic diversity information has recently become an important tool in conservation science. This paper aimed to determine the genetic diversity of the bamboo borer larvae in the Mau Forest complex in order to generate information that could guide the management and conservation of bamboo trees (Yushinia Alpina) in the Mau Forest Complex. The mitochondrial C oxidase Subunit 1 (COI) of 12 isolates was sequenced and analyzed. A similarity search of the bamboo borer larvae was carried out using the National Center for Biotechnology Information (NCBI) BLAST search to identify the larvae species. The genetic diversity and genetic pairwise distances were determined, and Tajimas D and Nei’s FU Fs statistics were calculated to estimate the population expansion that has occurred. The results showed genetic diversity (haplotype diversity 0.956) in the bamboo borer larvae population of the Mau Forest Complex. The nucleotide diversity (0.283) was found to be low. The similarity search showed that the bamboo borer larvae of Yushinia alpina belonged to four (4) species of noctuid larvae (Lepidoptera). The identity matches to the similar species scored an average of 94%. The Tajimas D (0.374) and FUs Fs (5.547) collectively indicated no rare excess mutations in the population. The results reveal high genetic diversity, which is key in the management of forest species.