Using (RAPD), (AFLP), Simple Sequence Repeats (SSR) and morphological traits, two DNA marker maps for C. pepo were constructed. In total 333 and 323 markers were mapped in zucchini and crookneck maps, respectively. The two populations shared 92 loci, 62 of which were mapped. These loci enabled the comparison of the two maps and established homology between 14 linkage groups. Some of these markers could play the role of anchor loci for C. pepo. Bulked Segregant Analysis (BSA) identified seven markers linked to the seed coat character (less than 7 cM) in the zucchini population. One of these markers was found linked to the seed coat (less than 4 cM) in the crookneck population. Two (Sequence Characterized Amplified Region) SCAR markers linked to Zucchini Yellow Mosaic Virus (ZYMV) resistance genes were mapped in the zucchini map in two different linkage groups together with a number of clustered loci originating from the source of resistance Cucurbita moschata.