THE GENETIC variation and relationships among 16 pumpkin accessions of Cucurbita moschata & Cucurbita maxima were assessed based on variation in fruit shape, skin color, flesh and size of fruits. Polyacrylamide gel electrophoresis of seed protein and molecular markers revealed by SCoT and ISSR techniques. The SDS-PAGE electropherogram showed 12 bands; two (75 and 145 kDa) were found in accessions (1-8) and one (85 kDa) was found in accessions 9-16. Other three bands were unique to accessions 1, 2 & 11. Five ISSR primers produced 79 markers ranging in molecular size from 130 to 2140 bp. Six SCoT primers produced 173 markers ranging from 135 to 2660 bp. The ISSR polymorphism among the examined accessions was 100% in the case of primers 49A, 44 B and HB-12, and was 92% for primer HB-15. Similarly, 100% polymorphism was scored for the primers SCoT8, SCoT11, SCoT12 and SCoT14. The lowest polymorphism was 93.94% in case of primer SCoT1. Our data based on protein, RAPD and ISSR data using the SYSTAT version 7.0 program clearly distinguished accessions from each other.