Moth bean is a small-seeded, protein-rich, and abiotic stress-resilient legume grown in arid and semi-arid areas of South Asia. Cultivation of this underutilized legume can reduce the dependency on commercialized Vigna species for food and nutrient security in underdeveloped countries. However, low yield remains one of the major limitations in the wider adoption of the crop among farmers in South Asian countries. To address this challenge, the present study employs genome-wide association studies to dissect the genetic basis of seed weight, a very important trait directly related to seed size and yield. The study used a diverse panel of 327 genotypes, which were phenotyped for 100-seed weight trait across three environments. By employing four multi-locus GWAS methods and 8518 SNP markers, we identified 17 significant SNPs across the genome associated with seed weight. The important seed size/seed development-associated candidate genes anchoring these SNPs were S-protein-like protein, purple acid phosphatase, kinetochore protein spc25 isoform X2 and CBL-interacting protein kinase 8-like protein. Four trait-associated SNPs/genomic regions identified in this study exhibited significant effects on the 100-seed weight trait. Genes associated with two of these SNPs (SNP2374: "g20155.t2" encoding purple acid phosphatase, and SNP5696: "g29506.t1" encoding kinetochore protein spc25 isoform X2) showed prominent upregulation in flower and early developing seed tissues/pod development stages suggesting their role in regulating seed size in moth bean. Trait-based markers developed from these candidate genes could potentially accelerate the marker-assisted breeding program to enhance seed weight and overall productivity of moth bean.