A linkage map was constructed of the watermelon genome using F2 and F2:3 populations segregating for resistance to race 1 and 2 of Fusarium oxysporum f. sp. niveum (FON 1 and 2). Sixty-four percent of the RAPD primers used in the parents and F1 detected polymorphism. In the F2, 143 polymorphic bands were scored, 60% of which exhibited the expected 3:1 segregation ratio. A 113 cM linkage map was constructed using Mapmaker version 3 and LOD of 4. DNA pools of Fusarium wilt resistant or susceptible F2:3 lines were created and bulked segregant analysis was used to detect molecular markers linked to FON 1 or FON 2 resistance. Four individuals per line were used to confirm linkages and construct an F2:3 linkage map. One large linkage group was detected in both generations. A large proportion of the RAPD and SSR markers were unlinked and many showed segregation distortion. Single-factor ANOVA for each pairwise combination of marker locus and resistance or morphological trait was conducted. RAPD markers with putative linkages to FON 1 and FON 2 and several morphological traits were detected.