Previous linkage analyses of 19 cutaneous malignant melanoma/dysplastic nevi (CMM/DN) kindreds showed significant evidence of linkage and heterogeneity to both chromosomes 1p and 9p. Five kindreds also showed evidence of linkage (Z>0.7) to both regions. To further examine these findings, we conducted two-trait-locus, two-marker-locus linkage analysis. We examined one homogeneity and one heterogeneity single-locus model (SL-Hom and SL-Het), and two-locus (2L) models: an epistatic model (Ep), in which CMM was treated as a genuine 2L disease, and a heterogeneity model (Het), in which CMM could result from disease alleles at either locus. Both loci were modeled as autosomal dominant. The LOD scores for CMM alone were highest using the SL-Het model (Z = 8.48, theta = .0). There was much stronger evidence of linkage to chromosome 9p than to 1p for CMM alone; the LOD scores were approximately two times greater on 9p than on 1p. The change in LOD scores from an evaluation of CMM alone to CMM/DN suggested that a chromosome 1p locus (or loci) contributed to both CMM and CMM/DN, whereas a 9p locus contributed more to CMM alone. For both 2L models, the LOD scores from 1p were greater for CMM/DN than for CMM alone (Ep: Z=4.63 vs. 3.83; Het: 4.94 vs. 3.80, respectively). In contrast, for 9p, the LOD scores were substantially lower with CMM/DN than with CMM alone (Ep: 4.64 vs. 7.06; Het: 5.38 vs. 7.99, respectively). After conditioning on linkage to the other locus, only the 9p locus consistently showed significant evidence for linkage to CMM alone. Thus, the application of 2L models may be useful to help unravel the complexities of familial melanoma.