Continuous human-mediated introduction of colonies and queens promotes genetic introgression and reshapes the genetic diversity and structure of local honeybee populations. According to reports, multiple non-native honeybee colonies and queens have been introduced into the DL region, leading to continuous genetic introgression. Here, we assessed the effects of continuous introgression on indigenous Apis cerana in the DL region using mtDNA and genome-wide SNP markers. We sequenced the mitochondrial tRNA ^leu-COII from 217 individuals sampled at 7 DL sites and identified 26 haplotypes defined by 18 polymorphic sites. The ΦST values indicated no internal differentiation within the Apis cerana populations in the DL region. Phylogenetic, network, ABBA-BABA test, and f3 statistic suggested introgression from both northern and southern sources. The f4-ratio indicates that approximately 16% of the ancestry in the DL group is derived from the Aba group. Genetic diversity varied widely within the DL region (Hd: 0.2907–0.8220; π: 0.0009–0.0038; K: 0.3140–1.3980), indicating different stages of introgression. The genetic structure within the DL group appears to be unstable, necessitating long-term monitoring of evolutionary processes and genetic diversity dynamics in A. c. cerana for further insights.