An earlier program of ours, TetraploidMap for Windows, enabled linkage analysis and quantitative trait locus (QTL) interval to be carried out in an experimental cross of an autotetraploid species, using both dominant markers such as AFLPs and codominant markers such as SSRs. The size was limited to 800 markers, and QTL mapping was conducted for each parent separately due to the difficulties in obtaining a reliable consensus map for the two parents. Modern genotyping technologies now give rise to datasets of thousands of single nucleotide polymorphisms (SNPs), and these can be scored in autotetraploid species as SNP dosages, distinguishing among the heterozygotes AAAB, AABB and ABBB, rather than simply using the presence or absence of an allele. The dosage data is more informative about recombination and leads to higher density linkage maps. The current program, TetraploidSNPMap, makes full use of the dosage data, and has new facilities for displaying the clustering of SNPs, rapid ordering of large numbers of SNPs using a multidimensional scaling analysis, and phase calling. It also has new routines for QTL mapping based on a hidden Markov model, which use the dosage data to model the effects of alleles from both parents simultaneously. A Windows-based interface facilitates data entry and exploration. TetraploidSNPMap is freely available from the web site of Biomathematics and Statistics Scotland at http://www.bioss.ac.uk/knowledge/software.html .