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Tomato yellow leaf curl disease is a serious production problem to tomato and other economically important crops. It is caused by Tomato yellow leaf curl virus transmitted by sweet-potato whitefly. All breeding for TYLCV resistance is derived from an introgression of Ty-1 from S.chilense line LA1969. This study was designed to find new resistance genes introgressed from three wild tomato accessions (S.peruvinum LA2172, S.Chilense G.1.1556 and S.Chilense G1.1558). A total of 84 SSR, CAPS and SCAR markers were screened for the mapping population using BSA approach. Marker screening of S.peruvianum LA2172 derived mapping population revealed two candidate markers on chromosome 5 and 11 linked to the resistance gene on pooled DNA. Further analysis of the two candidate markers on individual plants showed that, marker on chromosome 11 linked to Ty-2 which was mapped by Hanson et al, 2006, whereas; marker on chromosome 5 was not linked to the resistance gene. Markers screening of S.Chilense G1.1556 and S.Chilense G1.1558 derived mapping populations exhibited no linked markers. Therefore, the study is important for breeding companies as well as scientific communities working in the area.