Grass pea (Lathyrus sativus L.) is an important food crop cultivated in dryland agricultural ecosystem. It is an important source of dietary protein to millions of people living in low-income countries in South-east Asia and Africa. The present study emphasises the development of genomic resources and their application in marker–trait association for plant phenology and yield-related traits in lathyrus. In silico mining of nucleotide sequences identified 203 simple sequence repeat (SSR) motifs, of which trimer repeats (62%) were most abundant followed by tetramer (19%), hexamer (10%), pentamer (6%) and dimer (3%) nucleotide repeats. Of 150 SSR markers screened, 60 markers were amplified 75 alleles from 50 germplasm lines with 2–3 alleles per locus and the polymorphic information content of 0.45 was observed. We report 6 significant marker–trait associations using the developed SSR markers for plant phenology and yield-related traits following mixed linear model (Q+K) analysis. Gene ontology search of trait linked markers revealed marker regions encoding genes related to homeobox-leucine zipper protein ATHB-6-like, rubredoxin family protein, and cationic peroxidise. Understanding the association of novel alleles in trait expression will play a significant role in future lathyrus crop improvement programmes.