Association mapping of qualitative and quantitative characters is useful for finding gene markers and have not been reported in watermelon. The objective of this study was to detect molecular markers associating with 19 plant and fruit related traits such as number of branches and seed coat color. Ninety-six watermelon lines were selected from 259 accessions selfed 4 to 6 times available in germplasm resources. Sequence related amplified polymorphism (SRAP) primer combinations selected from 208 combinations were used to study 259 watermelon lines available in the Turkish genetic resources. The number of watermelon lines was reduced to 96 to eliminate highly identical ones based on Dice coefficient and UPGMA tree nested in NTSYS software PC version 2.1. This result indicated that most watermelons available in this germplasm were highly related. Morphological evaluations were performed at the University of Cukurova in Adana. Population structure data were obtained using "STRUCTURE" software. Association analyses are being performed using the "TASSEL" software to identify molecular markers associated with 19 important watermelon traits. Using a SAS program, regression analysis is being performed to exclude redundant markers at the alpha 0.10 level. Our preliminary results indicate that association mapping to identify molecular markers associated with phenotypic qualities is possible with watermelon lines.