The genome sequences of Salinas （lettuce） and YL1 （stem lettuce） were compared to elucidate the genetic differences among the main cultivated types of lettuce （Lactuca sativa） including crisphead lettuce，Youmaicai，and stem lettuce and resolve the issue of synonymy.23 901 potential InDel loci were identified across the whole genome.80 loci were randomly selected for designing primers.42 stably polymorphic markers were obtained from screening with PCR across six accessions of stem lettuce and six accessions of lettuce.57 commercial varieties including 10 crisphead lettuce，24 stem lettuce，and 23 Youmaicai were subsequently genotyped with polymorphic markers obtained.The results showed that the number of markers suitable for distinguishing crisphead lettuce，stem lettuce，and Youmaicai was 14，17，and 35 out of the 42 polymorphic markers，respectively.The 10 varieties of crisphead lettuce were classified into 8 groups，the 24 varieties of stem lettuce into 20 groups，and the 23 varieties of Youmaicai into 12 groups，meaning that there are genetic differences and synonymy among varieties.It is indicated that the developed InDel marker system can be directly used for the rapid identification and clarification of genetic background in varieties of lettuce.