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Smiliogastrinae are recognized for their high nutritional and ornamental value. In this study, we employed high-throughput sequencing technology to acquire the complete mitochondrial genome sequences of <i>Dawkinsia filamentosa</i> and <i>Pethia nigrofasciata</i>. The gene composition and arrangement order in these species were similar to those of typical vertebrates, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region. The mitochondrial genomes of <i>D. filamentosa</i> and <i>P. nigrofasciata</i> measure 16,598 and 16,948 bp, respectively. Both <i>D. filamentosa</i> and <i>P. nigrofasciata</i> exhibit a significant preference for AT bases and an anti-G bias. Notably, the AT and GC skew values of the ND6 gene fluctuated markedly, suggesting that the selection and mutation pressures on this gene may differ from those affecting other genes. Phylogenetic analysis, based on the complete mitochondrial genomes of 23 Cyprinidae fishes, revealed that <i>D. filamentosa</i> is closely related to the sister group comprising <i>Dawkinsia denisonii</i> and <i>Sahyadria chalakkudiensis.</i> Similarly, <i>P. nigrofasciata</i> forms a sister group with <i>Pethia ticto</i> and <i>Pethia stoliczkana</i>.