Linkage maps facilitate the study of the genetic architecture of reproductive isolation. We constructed a map for newts of the Lissotriton vulgaris species complex: 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM. A complex pattern of transmission ratio distortion (TRD) was detected, consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in two genomic segments; this suggests a role of TRD blocks in reproductive isolation. The linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.