Natural selection, driven by various living conditions, plays a crucial role in shaping biased codon usage in genomes and organelle genomes. Despite the Chironomidae having thousands of species inhabiting a variety of habitats, codon bias in species of the family remains poorly understood. In this study, we sequenced the novel mitogenome of Microtendipes umbrosus Freeman, 1955 and conducted a comprehensive analysis of its codon usage. The assembled mitogenome is 15,827 bp and contains 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and an A+T-rich noncoding region. The overall nucleotide composition is 40.6% A, 39.8% T, 11.6% C, and 8.0% G, with an A+T bias of 80.4%. Interestingly, all PCGs except cox1 (TTG) commenced with ATN codons, and all terminated with the TAA codon. Relative synonymous codon usage analysis indicated a high frequency of codons with A or U in the third position. In the PCGs, a total of 22 codons are overrepresented, while 27 codons are underrepresented. Notably, four codons, AGG, CGC, CUC, and CUG, are completely absent. The neutrality plotting analysis, the parity rule 2 plotting analysis, and the effective number of codons analysis all demonstrated the influence of natural selection on the mitogenome of M. umbrosus. This investigation provides an essential DNA molecular database for further evolutionary and molecular research on Chironomidae.