The stingless bee Meliplebeia beccarii, endemic to Ethiopia, plays a crucial ecological and economic role through pollination and high-quality honey production. However, habitat degradation and anthropogenic pressures threaten its survival. In this study, we present the complete mitochondrial genome (mitogenome) of M. beccarii, revealing a compact structure of 15,458 bp with 13 protein-coding genes (PCGs), 19 tRNAs, and two rRNAs, characterized by an A + T bias (83.9%). Unique features include the absence of trnI, trnK, and trnA, translocation of trnQ and a novel inversion in the trnT-trnP combination. These findings highlight species-specific genomic adaptations. Phylogenetic analysis based on concatenated PCGs places M. beccarii within the Apidae lineage, contributing to a deeper understanding of stingless bee evolution. Our results underscore the utility of mitogenomic studies in biodiversity conservation and evolutionary biology, providing foundational insights for the management and preservation of M. beccarii.