Foxtail millet (Setaria italica L. Beauv.) is a grain-producing crop with high nutritional benefits and adaptability to broad environmental conditions. Indonesian local foxtail millet accessions are valuable genetic resources for crop improvement of the species. This study aims to assess the biodiversity of Indonesian local foxtail millet accessions and estimate their salinity tolerance level utilizing the SiDREB2-based SNAP marker and early evaluation at the seedling stage. Our results showed that eight Indonesian local foxtail millet accessions, namely Toraja, Mauliru-2, Hambapraing, NTB-1, ICERI-5, ICERI-6, Botok-4, and Botok-10, had high variability based on agro-morphological traits. The Hambapraing and Mauliru-2 were the potential accessions with high yield estimates (2.33 ton.ha-1 and 1.93 ton.ha-1) and early harvest time (