Lettuce (Lactuca sativa), as a globally important vegetable crop, mainly includes leaf types (such as lettuce and celtuce) and stem types (stem lettuce). China, being the world's largest lettuce producer, accounts for over 50% of the global total in terms of both cultivation area and yield. However, lettuce breeding in China faces challenges such as severe cultivar homogenization and synonymy issues, which significantly hinder the protection of new varieties and industry development. In this study, by comparing the genome sequences of lettuce cultivar Salinas and stem lettuce cultivar YL1, we systematically identified 23,898 potential insertion/deletion (InDel) loci across the whole genome. From these, 80 loci were selected for polymorphism validation, and the results showed that 42 InDel markers exhibited good polymorphism in six stem lettuce and six lettuce cultivars. Further analysis revealed that these markers have differential discriminative capabilities among different cultivar types: 14 markers were suitable for distinguishing heading lettuce cultivars, 17 markers were effective for stem lettuce cultivar identification, and 35 markers showed polymorphism in celtuce cultivars. Based on this marker system, we systematically analyzed 57 commercial cultivars (10 heading lettuce, 24 stem lettuce, and 23 leaf lettuce) with different market names. The results demonstrated that the 10 heading lettuce cultivars were classified into 8 groups, the 24 stem lettuce cultivars into 20 groups, and the 23 leaf lettuce cultivars into 12 groups, revealing genetic differences and synonymy among these varieties.The results not only provide efficient molecular marker tools for lettuce cultivar identification but also lay a crucial foundation for marker-assisted breeding and the formulation of new variety testing guidelines. This research holds significant practical value for promoting innovation and development in the lettuce seed industry.