Guar [Cyamopsis tetragonoloba (L.) Taub.] is a drought and heat tolerant annual legume and is the most economically important species in the Cyamopsis genus. Information about the genetic relationships among the commercial cultivars is important for future guar breeding programs. Eight accessions including 6 guar commercial cultivars and 1 plant introduction (PI) each of C. senegalensis and C. serrata, respectively, were studied with UPGMA (unweighted pair group method using arithmetic averages) clustering analysis using random amplified polymorphic DNA (RAPD) and morphological data. The RAPD analysis identified a total of 29 bands among the three species, with 26 bands being polymorphic. The number of polymorphic bands amplified per primer ranged from 2 to 6, with a mean of 3.3. Cluster analysis grouped the 3 species into 2 distinct groups. Group 1 consisted of accessions from C. serrata and C. senegalensis, and group 2 consisted of the 6 guar cultivars. Within group 2, Kinman is more distant from the other 5 guar cultivars. Similar results were obtained using ten morphological characters while more variability was detected within group 2 compared with that of RAPD data. Due to the low variability and narrow genetic background of commercial cultivars of guar, more guar germplasm should be introduced in order to breed out new guar cultivars.