Genetic research is an important key in carrying out conservation and sustainable management of a species. Sicyopterus macrostetholepis(known locally as the mungkuih fish) does not yet have sufficient genetic data and is included in the IUCN Red List of Threatened Species. This research aimed to determine the phylogenetic relationship of the mungkuih fish population, thought to be endemic, in Padang City, West Sumatra. Sampling was carried out in Batang Kuranji, Batang Air Dingin and the Lubuk Hitam River during June-August 2021. Molecular analysis through the stages of extraction, PCR, electrophoresis and DNA sequencing, was conducted. DNA sequence analysis was conducted using MEGA XI (Genetic distance, Phylogenetic), DNASP (Haplotype) and arlequin (Fixation index, Amova). The research found a fragment length of 773 base pairs. Genetic distance analysis of mungkuih fish was 0.25-1.12%. The phylogenetic tree shows that the divergence between the outgroup and the Gobiidae family is 21.78-28.01%. The analysis value of the fixation index (Fst) was 0.47977 showing the high genetic heterogeneity between the mungkuih fish populations in Padang City, as can be seen from the Haplotype and AMOVA tests. The haplotypes obtained in this study were h=7 and Hdt =0.944. The results show that Haplotype and Fst indicate that the genetic structure of the mungkuih population in Padang City is not disturbed.