Karyotype characters, mitotic metaphase chromosomes, monoploid idiograms, karyograms and pollen abortion of Lotus creticus L., Lotus glaber Mill., Lotus halophilus Boiss. and Lotus peregrinus L. were investigated. Analysis of somatic metaphases showed that the chromosome numbers of these taxa were 2n=28 for L. creticus, 2n=12 for L. glaber, 2n= 14 for both L. halophilus and L. peregrinus. Karyotype asymmetry was estimated by many different methods, the total form percent (TF %), the Rec and Syi indices, the intrachromosomal asymmetry index (A1) and interchromosomal asymmetry index (A2). In this study, there is a variation in the frequency of pollen fertility and abortive pollen grains of the Lotus species. The anatomical characteristics of leaf and stemof Lotus species were made. Various genetic markers have been used to estimate the genetic variability within and among the four Lotus species collected from ten different accessions. Protein profile of Lotus species were studied by polyacrylamide gel electrophoresis (SDS-PAGE) technique and generated seventeen bands, six of them monomorphic and eleven polymorphic bands. Five tested primers were used for RAPD technique, a total of 33 well-defined and scorable RAPD bands were obtained as a result of fingerprinting of Lotus species, 12 bands were common for all species and 21 were polymorphic. Perceptual mapping (PERMAP) used for the combination of taxa and attributes PERMAP-Biplot distinguished the taxa into three groups.