A high sucrose clone S. officinarum ‘Gungera’ and a low sucrose clone S. spontaneum ‘SES 603’ were crossed to obtain interspecific hybrids named as ISH-1 to ISH-29 and graded into very high, high, low and very low sucrose types The objectives of present investigation were to compare high and low sugar genotypes, as also, their progeny for sucrose content, and to identify molecular markers for sucrose accumulation in sugarcane. Simultaneous work was carried on six selected commercial sugarcane cultivars also. Protein markers obtained in SDS-PAGE showed presence of a protein band of MW 19.95 kD in high sucrose types. Commercial sugarcane var. Co 7717 showed presence of a total 37 bands, of which protein bands of MW 100, 87.09, 83.17 and 81.28 kD were highly specific. DNA markers for high and low sucrose were identified. Of the ten microsatellite primers selected, four SSRs distinguished high and low sucrose markers. SSR primer AI, A and B amplified high sucrose markers and SSR primer SMC226CG+ SMC226CG amplified a low sucrose marker.