QTL mapping gives an insight into the number, position and effect of loci controlling quantitative traits. Although a few linkage maps already exist for papaya, not many economically important traits have been studied. An investigation was undertaken to map two qualitative traits: 1) fruit flesh color and 2) an isozyme locus, phosphoglucomutase (PGM); as well as two quantitative traits: 1) number of nodes to first flowering and 2) stamen carpellody. An F2 population consisting of 281 plants derived from the parents Kapoho X Saipan Red was used for this study. Field observations suggested that there may be a linkage between PGM locus and one of the major QTLs controlling number of nodes to first flowering. Also, phenotypic data suggested that there may be a linkage between flesh color and carpellody. Marker genotyping was performed on a subset of 84 plants chosen from the phenotypic extremes of the population for node number and carpellody. Using AFLP (Amplified fragment length polymorphism) method, 510 markers were generated with 161 primer pairs. Although papaya has a haploid chromosome number of 9, at LOD score 5.0 and a maximum recombination frequency of 0.25, 25 linkage groups with number of markers ranging from 2 to 109 were generated using the software Mapmaker\EXP. Linkage and QTL maps are being constructed to reveal the molecular markers linked with the traits of interest and the nature of QTLs controlling the quantitative traits.