A candidate gene exhibiting pleiotropic effect on twelve different seed size and weight traits was identified through a combination of evidence from population genetic selection, GWAS, earlier QTL studies, transcriptome analysis,  and transgenic analyses. Peanut is an important oilseed crop. Seed weight and size significantly impact yield, leading to the identification of numerous QTLs associated with these traits. However, due to the complexity of the genetic basis of these traits in peanut, still lots of work awaits to be done. Here, we conducted whole-genome resequencing of 183 peanut germplasms with abundant genetic variation. Subsequently, GWAS analysis was performed to investigate 12 traits related to seed size and weight, identifying two peak SNP clusters located on chromosome 6 and 16 that showed potential pleiotropic effects. We calculated XP-CLR scores across the genome, compared nucleotide diversity levels between modern improved cultivars and landraces, and identified 24 selective sweep regions. A significant majority (~ 83%) of these regions were primarily located on Arahy.16. Candidate regions on Arahy.16 have also been frequently identified in previous seed studies. The presence of all evidence prompted us to conduct a more extensive investigation of Arahy.16. Within the candidate genes located in the peak SNP cluster on Arahy.16, our transcriptome analysis revealed that 36 of them, including a highly promising candidate gene encoding a flavin-binding monooxygenase family protein (FMO), exhibited differential expression between small- and big-seed. Functional analysis revealed that Arabidopsis plants with an overexpressed FMO allele exhibited a significant increase in seed size and weight. In summary, the results could help the peanut researchers to gain a better understanding of the genetic basis of seed traits and may hold significant potential for future cultivar improvement.