Job’s tears (Coix lacryma-jobi L.) is a nutritious food crop with potential health benefits and has been used for a long time for treating inflammatory diseases. The objective of this study was to evaluate the genetic diversity of 20 Job’s tears accessions collected from the Northwest regions in Vietnam using morphological traits and molecular markers. Based on the morphological trait analyses, the 20 genotypes were grouped into two clusters at a Euclidean distance of 3.5. Cluster I included four accessions with hard, thick glume and fruit, and cluster II consisted of 16 accessions with dark gray seeds at full ripeness. Of the 17 SSR markers, seven were found to be polymorphic, generating 28 polymorphic bands over seven SSR loci. The average number of alleles per locus was 4.0, and the PIC value ranged from 0.46 to 0.75, with an average of 0.63. The Dice's similarity coefficient ranged from 0.84 to 1.0. However, the Mantel test revealed a low correlation between the morphological and molecular matrices, indicating differences in the relationships between morphological traits and molecular markers. Both the morphological and molecular approaches provided useful information for breeding programs and germplasm utilization in Vietnam. Overall, this study may contribute to a better understanding of the genetic diversity of Job’s tears, which is essential for future crop improvement programs.