Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth.  However, the genetic mechanism underlying seed size in melon remains unclear.  In the present study, we employed Bulked-Segregant Analysis sequencing (BSA-seq) to identify a candidate region (~1.35 Mb) on chromosome 6 that corresponds to seed size.  This interval was confirmed by QTL mapping of three seed size-related traits from an F₂ population across three environments.  This mapping region represented nine QTLs that shared an overlapping region on chromosome 6, collectively referred to as qSS6.1.  New InDel markers were developed in the qSS6.1 region, narrowing it down to a 68.35 kb interval that contains eight annotated genes.  Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002, a leucine-rich repeat receptor-like kinase (LRR-RLK) gene.  This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions (C-allele) from the small-seeded accessions (T-allele).  qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines.  Its predicted protein has typical LRR-RLK family domains, and phylogenetic analyses reveled its similarity with the homologs in several plant species.  Altogether, these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation.  Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.