Species of the genus Tulipa L. (Liliaceae) are characterized with a high variability of vegetative and floral characters, which makes the taxonomy of this genus difficult. In Kosovo the genus Tulipa is represented by eight taxa, which sometimes have been synonymized, erroneously identified, or misclassified. To investigate the phylogenetic relationships of Tulipa species originated from Kosovo, ITS and trnL-trnF DNA sequences were used. In total 55 sequences (29 ITS and 26 trnL-trnF), obtained from 14 taxa were analysed. Forty one sequences were newly generated from eight taxa collected from wild population in Kosovo and 14 sequences were obtained from GenBank. Neighbor-Joining, Maximum Parsimony and Maximum Likelihood trees from independent (ITS and trnL-trnF) and combined (ITS + trnL-trnF) datasets were conducted in PAUP. Based on sequence analyses, our sequences of Tulipa species grouped into two main clades, belonging to the subgenera Eriostemones and Tulipa, respectively. There is not sufficient genetic evidence to distinguish species of the T. scardica complex (T. scardica, T. serbica, T. albanica, T. kosovarica and T. luanica) as independent taxa. Despite the lower resolution of the trnL-trnF than the ITS dataset, both loci do not support the separation of taxa of the T. scardica complex as independent species.