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Simple Summary: Chironomidae is ecologically an important family within the order Diptera. With the rapid advances in next-generation sequencing technologies, an increasing amount of mitochondrial genome data for chironomids has been published. The phylogenetic relationships between the three relatively large and morphologically similar genera within the Harnischia generic complex, namely Cryptochironomus, Demicryptochironomus, and Harnischia, have yet to be thoroughly investigated. The comprehensive mitotic genomes of 11 species within this generic complex were sequenced. Our findings indicate that the monophyly of the genus Harnischia is strongly supported across all topologies, revealing that Cryptochironomus is a sister taxon to Demicryptochironomus. This represents a new insight into the systematic study of the Harnischia generic complex. (1) Background: Mitochondrial genomes have been extensively employed as a crucial marker in numerous dipteran families for understanding phylogenetics and systematics relations, thereby playing a pivotal role in molecular biology studies. The phylogenetic relationship of the Harnischia generic complex remains contentious due to the paucity of taxonomic and molecular data. Specifically, the evolutionary relationships among Cryptochironomus, Demicryptochironomus, and Harnischia are still unclear. (2) Methods: In this study, Polypedilum and Endochironomus were used as outgroups to analyze phylogenetic relationships among Cryptochironomus, Demicryptochironomus, and Harnischia, mitogenomes of four Cryptochironomus, two Demicryptochironomus, two Harnischia, and two Cladopelma were newly sequenced. Subsequently, we conducted a thorough analysis of the nucleotide composition, sequence length, and evolutionary rate. (3) Results: All mitogenomes exhibited structural conservation, with all genes consistently arranged in the identical order as that of the ancestral mitogenome. Nucleotide composition varied significantly among different genes, and the control region displayed the highest A + T content. All protein-coding genes undergo rigorous purification selection, with the ATP8 gene exhibiting the most rapid evolutionary rate among them. Utilizing Bayesian Inference (BI) and Maximum Likelihood (ML) methods across various databases, we reconstructed the phylogenetic relationships among the genera within the Harnischia generic complex, drawing insights from an analysis of 14 mitochondrial genomes. (4) Conclusions: Our results showed that the monophyly of the genera Harnischia was well supported in all topologies; Cryptochironomus is sister to Demicryptochironomus. [ABSTRACT FROM AUTHOR]