Due to the unique blue color and perennial growth habit, Muscari can be cultivated as a bedding plant, pot plant, or cut flower. Meanwhile, there is lack of information about genetic variations of Muscari neglectum Guss. ex Ten.; consequently, the diversity of nine populations (90 accessions) belonging to M. neglectum was evaluated by inter simple sequence repeat (ISSR) marker, start codon targeted (SCoT) marker and morphological marker. Ten ISSR primers used in this experiment amplified 142 reproducible bands with 137 (96.4%) polymorphism; and ten SCoT primers amplified 165 bands with 151 (91.12%) polymorphism. Both ISSR and SCoT analyses indicated a high level of genetic variation in the wild population of M. neglectum. Analysis of Molecular Variance (AMOVA) revealed a higher genetic diversity within the geographic group (0.69%) compared to the genetic variation among populations (0.31%). The gene flow between populations was low, while there was a greater gene flow between close areas. Morphological data divided nine populations into three clusters, while molecular data separated the populations into five groups, which were confirmed with structure analysis and discriminant analysis of principal component (DAPC) analysis. Our investigation showed that first, SCoT and ISSR markers are suitable for evaluation of genetic variation in Muscari genus, and there is appropriate genetic diversity among M. neglectum populations. Our results suggest some information to conserve the genetic resources and improve breeding program based on genetic data.