A number of biotic and abiotic stress factors effect sugarcane yield. Some internal factors like endogenous gibberellins, protein and RNA are known to govern the flower formation. An increase in the protein and nucleic acid content during the transformation of the meristem from the vegetative to reproductive state will affect the sugarcane yield. Study was undertaken with two flowering sugarcane varieties (BO 91 and CO H 15) with a view to investigate the effect on molecular changes. Isolation of RNA, Reverse Transcription and PCR Amplification with DNA Polymerase were done and the expression of all the three genes (Acid Invertase, Sucrose Phosphate Synthase 1 and Sucrose Phosphate Synthase 2) under study was confirmed and they were 200bp (Acid Invertase, Sucrose Phosphate Synthase 1) and 600 bp (Sucrose Phosphate Synthase 2) in size.