Abstract: Two sugarcane varieties, V1 (an early maturing) and V2 ( a mid-late maturing) were planted during spring season of 2014 in tray culture conditions at IMS Engineering college, Ghaziabad with an objective to study the effect of short term waterlogging on growth and physio-biochemical attributes, RNA isolation and expression of SOD (superoxide dismutase) using gene specific primer pairs. After about 60 days of planting, waterlogging stress treatment was imposed to plants by transferring planted pots in a bucket filled with water. Treatments consist of control 48, 96 hr. of waterlogging stress and recovery after 2 days of termination of treatments. Observations were recorded for SPAD Reading, RWC, chlorophylls and carotenoid contents, proline, and activity of SOD and peroxidase enzymes, soluble protein content and Cu-Zn-SOD gene expression.