Genomic tools for watermelon studies are becoming increasingly available. In order to utilize DNA markers in marker assisted breeding, a high throughput genotyping system is desirable. A leaf-based genotyping system that requires prior germination of seed is often time-consuming and cost prohibitive. In an effort to develop an efficient system, watermelon seeds of several genotypes with different seed sizes were sampled by cutting off the distal end-portions while germinating the remaining proximal-end portions. The results indicated that cutting off 1/3 of the seed at the distal end had no effect on the germination rate of the seed. Different DNA extraction protocols were tested to identify a method that yielded good quality DNA from the distal end-portions. A sodium dodecyl sulphate based extraction protocol yielded DNA that could be amplified using microsatellite markers. In this study, an efficient, non destructive genotyping protocol from watermelon seed was developed.