The systematic status of the genus Cyclocheilichthys remains ambiguous due to a lack of comprehensive morphological and molecular evidence. Hence, this study represents the novel mitogenome of Cyclocheilichthys repasson to characterize its architecture and clarify its phylogenetic placement within the clade "Poropuntiinae." The circular mitogenome was 16,571 base pairs in length and comprised 37 genes and a control region (CR). Most genes were encoded on the heavy strand, with the exception of ND6 and eight tRNA genes located on the light strand. The genome exhibited an A + T bias of approximately 57.7% and displayed distinct AT- and GC-skew patterns. All protein-coding genes (PCGs) initiated with the standard ATG start codon, except for COI, which began with GTG. The amino acid composition was dominated by leucine, serine, threonine, and isoleucine, and the ratio of nonsynonymous to synonymous substitutions suggested strong purifying selection across all PCGs. The majority of transfer RNA genes exhibited the canonical cloverleaf secondary structure, with the exception of tRNA-Ser, which lacked the dihydrouridine (D) stem. The comparative analysis of 24 "Poropuntiinae" species revealed four conserved sequence blocks within the CR, while tandem repeat motifs were exclusively detected in 11 species and absent in C. repasson. The mitogenome-based phylogenetic analyses using Bayesian and Maximum Likelihood methods supported the monophyly of Cyclocheilichthys and sister relationship of C. repasson with C. janthochir and C. apogon. The partial COI-based investigation further revealed potential cryptic diversity within C. repasson populations from both mainland (Laos) and island (Sumatra, Indonesia), as indicated by a genetic divergence of 1.06%. This population separation may have been influenced by historical paleo-river networks across Southeast Asia/Sunda Shelf during periods of lower sea levels. Collectively, these findings offer valuable insights into the structural features of the mitochondrial genome and elucidate the evolutionary history among cyprinid fishes.