Despite the ecological and genetic value of native legumes, their seed protein composition has received far less attention than that of cultivated crops. Therefore, we characterized the seed proteins from 18 native Korean Fabaceae species representing both woody and herbaceous taxa using nano LC-MS/MS. The analysis yielded 163 protein hits, assigned to seven functional groups. Unknown proteins comprised 39.3% of the total protein hits, whereas proteins related to metabolism and seed storage accounted for 25.2% and 16.0%, respectively. Storage proteins were mainly members of the 7S and 11S globulin families. Among individual proteins, β-conglycinin β showed the highest detection frequency, whereas canavalin, conglutin, and Concanavalin-Br were detected in a limited number of species. No clear difference in the detection patterns of major storage protein families was observed between woody and herbaceous species. Collectively, the results showed that major globulin families were detected across the examined species, while individual storage proteins exhibited variable detection patterns among species. This study provides comparative information on seed protein diversity in native Fabaceae species and a basis for further research on their taxonomic relationships, conservation, and utilization.