In this study, we tried to figure out phylogenetic relationships and taxonomical positions of closely related Muscari species. Four different cpDNA regions including both coding and non-coding ones, namely, matK, trnT((UGU))-trnL((UAA)) intergenic spacer (IGS), trnL((UAA)) intron and trnL((UAA))-F-(GAA) IGS, were employed to determine the exact circumscription of three subgenera, Muscari, Leopoldia and Botryanthus. Seventy Muscari accessions representing 31 Muscari species and different number of previously published sequences retrieved from NCBI database were analyzed. The concatenated and matK data alone were observed to be informative while none of the used non-coding regions was suitable to determine phylogeny of Muscari. Concatenated alignment gave almost the same tree topology with matK sequence. Muscari azureum and M. coeleste phylogenetically separated from all other species of Botryanthus and four main clades were observed in both of the trees even though three subgenera are accepted by Flora of Turkey. After discussing the phylogenetic positions and morphological characters in detail, moving of these two species from Botryanthus to Pseudomuscari subgenus was suggested. Thus, this study proposes that the number of Muscari subgenera should be increased from three to four in Flora of Turkey. The position of M. mirum was also remarkable; it always located distantly to its relatives of Leopoldia. Although this species may also be distinguished based on morphological features such as quite shorter plant length, one or sometimes two relatively wider leaves, and a larger fruit, it needs further studies to resolve its position reliably. Interesting positions of other species were also discussed in detail based on morphological characters in the text.