TLCV (Tomato leaf curl virus) is most destructive disease in tomato causes severe losses of up to 100%. It is transmitted by sole vector whitefly (Bemisia tabaci). Breeding of disease resistance is only truthful approach to combat the disease consists marker assisted selection (MAS). Therefore, the present investigation was carried out using of 110 F₂ mapping population individuals of cross ATL-97-26×GP-11. SSRs marker analysis was carried out to identify with a set of 374 SSRs were used for marker analysis. Parental polymorphic markers were utilized in genotyping of 110 F₂ mapping population individuals. Morphological and biochemically important traits like plant height, number of branches per plants, number of fruits per plant, disease incidence score, phenol content, moisture, total soluble Solids, terrible acidity, total soluble sugar, total flavonoids, lycopene and ascorbic acid content in 110 individuals of F_2:3 mapping population derived from cross of ATL-97-26×GP-11. The phenol content showed significant negatively correlation with disease incidence. Single marker analysis (SMA) found 9 marker trait association with above threshold level 3. The higher number of marker trait associations was found for phenol content and disease incidence. The phenol content and other morpho-biochemical traits are in current study can be exploited for develop hybrid of elite parental line/cultivars of tomato through marker assisted breeding programme. The SSRs markers i.e., TES0312, SSR112 and SSR331 identified from this study could be useful for TLCV resistance breeding in tomato.