The performance of 103 promising sugarcane lines/varieties under high inoculum conditions for whip smut, was checked over two successive cropping years. The yield potential of these sugarcane lines was evaluated in terms of their girth, height, weight, sugar recovery and smut resistance. Eighty-four (84) sugarcane lines were found highly resistant in the first year of cultivation while only 5 sugarcane lines were found susceptible. The sugarcane lines S.2003-US-127, S.2008-FSD-19 and S.2008-AUS-190 showed peak performance with respect to sugar recovery, cane weight and height respectively. The girth of sugarcane lines S. 2011-SL-813 and S. 2011-SL 209 was found maximum. However, during the second cropping year (ratoon crop), eighty (80) sugarcane lines were found highly resistant while only four (4) sugarcane lines were found susceptible. The performance of the sugarcane lines S. 2008-US-704, SPSG-24, S. 2011-SL-642 and S. 2011-SL-209 was found highest for sugar recovery, girth, cane height, cane weight, respectively during the second cropping year. Principal component bi-plot analysis reveals over all best performance of S.2008-FSD-17, S.2003-US-127, S.2008-US-704, S.2008-FSD-19 for all yield traits while overall least performance was recorded by S.2003-US-618, SPSG-27 for all the yield traits during both years of cultivation. Higher broad sense heritability and genetic advance values revealed in this study especially for cane weight and sugar recovery indicated that these traits could be utilized for developing hybrid and synthetic varieties. Significant negative impacts of whip smut were found upon the yield traits. However, these traits were found somewhat more genetically controlled with little to moderate environmental impacts. The LSD based ranking and other statistical analysis revealed high yield potential of these sugarcane lines for being used in future breeding programs. Understanding the level of genetic variability held in the sugarcane germplasm is critical for proficient use of its gene pool. Genetic diversity based response of 103 promising ii sugarcane lines/varieties for tolerance against whip smut was the main objective of this study. Genetic similarity coefficient ranging 66-88% observed in this study, indicated narrow genetic base of these sugarcane lines/varieties which arises the need of using distantly related sugarcane lines in breeding programs. DNAMAN generated dendrogram of 103 sugarcane lines and their response against whip smut will help in designing crosses between distantly related sugarcane lines/varieties that would not only increase the genetic base of sugarcane crop but would also help in developing whip smut resistant sugarcane cultivars. Also, varying response of sugarcane lines for smut resistance in the few clusters propose that whip smut resistance is neither confined to particular sub-population nor governed by genes with broad impacts but is in fact a genuine quantitative trait. Moreover, the genotyping files developed against the 314 amplified alleles of 30 markers especially against mSSCIR-43 and mSSCIR-19 would help sugarcane breeders in molecular identification of whip smut resistant and susceptible sugarcane lines. This would ensure correct clones involved in the crosses. High PIC and RP values of the tested markers highlighted their potential of using in in genetic diversity studies. Moreover, the genotyping data of all the 103 sugarcane lines/varieties against the amplified 314 alleles and the phenotypic data of two successive cropping years, was integrated using Structure 2.3.4 and TASSEL software to find the alleles linked with smut resistance and various yield traits. These linked alleles depicted phenotypic variance (R2-values) ranging from 3.1-24.6% for smut resistance, 2.67-22.5% for sugar recovery, 1.75-12.8% for sugarcane girth, 2.81-23.46% for cane height and 2.9-14.34% of cane weight. The maximum degree of association was revealed by the allele 52-121 for cane height, 82-184 for cane girth, 51-131 for sugar recovery, 51-145 and 51-146 for cane weight and smut resistance respectively. These alleles could help in marker assisted selection of studied sugarcane lines/varieties for these traits. The little effects of various linked alleles with smut resistance and yield traits indicated that these traits and smut resistance are controlled by additive effects of multiple genes.