Eruca sativa is an agronomically important oilseed crop with many industrial applications. The present study was undertaken to assess genetic relationships along with few phenotypic traits among 30 genotypes of E. sativa with PCR based ISSR primers. Fifteen ISSR primers were used and total of 168 reproducible bands were produced, of which 160 were polymorphic with an average of 10.6 polymorphic bands per primer. Discriminating power (D) ranged between 0.13 (IS- 9) to 0.98 (IS- 21) with an average value of 0.73. A high level of polymorphism was found in selected genotypes. Clustering was done using UPGMA analysis and the Eruca genotypes were distributed in six major clusters. The Jaccard's similarity coefficient was found in the range of 0.10-0.95. Nei's genetic distance was also estimated among the selected genotypes. The total oil content and major fatty acids of Eruca seed oil were measured in all genotypes. Erucic acid (EA) content of individual genotypes was correlated with cluster analysis and increasingly high EA containing genotypes grouped together in a single cluster. On the basis of our results, it can be concluded that RTM-577, RTM-789, RTM-1361 and RTM-1212 are the most diverse genotypes. Thus, these genotypes could be better candidates for industries and future breeding programs. (C) 2015 Elsevier Ltd. All rights reserved.