Seed coat color is an important agronomic trait that associates with crop domestication and serves as morphological marker. In mung bean, the seed coat color was related to the content of flavonoids. Cloning and application of seed coat color-related genes becomes of interest in development of new mung bean varieties with improved nutritional properties. In this study, the varieties ‘Jilv 9’ (black seed coat) and ‘Ziyuan 330’ (yellow seed coat) were used as parents to generate an F2 segregating population. The BSA-seq approach was applied for preliminary mapping of the genes underlying the seed coat color. The association analysis using integrated SNPs and InDels suggested an interval of 3.26 Mb harboring 324 predicted genes, of which 49 genes were found with non-synonymous mutations and 15 genes were detected with frameshift mutation. By further use of 11 high-quality KASP markers in fine mapping, the candidate interval was finally delimited between KASP330 and KASP421 in the physical interval of 16,302,330–18,013,421 bp (1.71 Mb) on chromosome 4. The transcriptome data analysis and qRT-PCR expression analysis suggested six differently-expressed candidate genes, of which the LOC106758748 was annotated as a transcription factor MYB90 that was reported with a function in the flavonoid biosynthesis and served as key candidate gene regulating the seed coat color in mung bean. This study laid a solid foundation for further cloning of mung bean seed coat color related gene(s) and the utilization in breeding.