The present investigation was carried out with three shoot fly resistant, one having recovery resistance and four susceptible genotypes and their twenty eight crosses. Out of 21 SSR primers used 6 were amplified and gave 12 bands and 327 clear fragments. Out of 12 bands 5 were polymorphic and level of average polymorphism was 41.67 per cent. The most informative band was of Xtxp 88 at 250 bp. The correlation between early vigour, glossiness and trichome density was significant positive. The average value of glossiness (p=0.00) and trichome density (p=0.02) was significantly low in the genotypes having Xtxp88 250 bp band. Correlation of marker Xtxp88 (250 bp) with glossiness (-0.58) and trichome density (-0.38) was significant and negative. In the stepwise regression analysis only one band Xtxp88 250 bp was entered and explained 33.20 and 14.70 percent variability of glossiness and trichome density, respectively, indicating that the band Xtxp88 250 bp was weakly associated with susceptibility to shoot fly.