In this study, the morphological, genetical (molecular) and elemental compositions of morphologically similar three endemic Lathyrus L. species such as L. phaselitanus Hub.-Mor. & Davis, L. lycicus Boiss. and L. belinensis N. Maxted & D. J. Goyder belong to genus Lathyrus in Turkey were investigated. In the morphological part, some important parameters such as stem shape, plant height, leaflet number, leaflet length, leaflet width, stipule shape, stipule length, stipule width, fruit length, fruit width, fruit shape, number of flowers and standard were investigated. In the genetical part of the study, chloroplast intergenic spacer trnH-psbA was used to reveal the genetic diversity and phylogenetic relationship among the three endemic Lathyrus species to decide whether they were systematically similar or not. Additionally, the concentration of some elements such as Nickel (Ni), Iron (Fe), Copper(Cu), Cadmium (Cd), Chromium (Cr), Manganese (Mn), Magnesium (Mg), Zinc (Zn), Sodium (Na) and Potassium (K) were also determined by flame atomic absorption spectrometry to observe the similarities and/or differences among these three endemic Lathyrus species based on elemental composition. The results revealed that there was also a genetic similarity of 99% between morphologically similar L. belinensis and L. lycicus species but they were previously placed in different sections.