|| Genetic linkage maps of the Japanese pear (Pyrus pyrifolia Nakai) cultivar 'Housui' and the European pear (Pyrus communis L.) cultivar 'Bartlett' were constructed based on Amplified Fragment Length Polymorphism markers (AFLPs), Simple Sequence Repeat markers (SSRs) (from pear, apple and Prunus), isozymes, and phenotypic traits by using their F1 progenies. The map of the female parent 'Bartlett' consisted of 256 loci including 178 AFLPs, 76 SSRs (32 pear, 39 apple, 5 Prunus SSRs), 1 isozyme and a self-incompatibility locus on 19 linkage groups over a total length of 1020 cM. The map of 'Housui' contained 180 loci including 110 AFLPs, 64 SSRs (29 pear, 29 apple, 6 Prunus SSRs), 2 phenotypic traits and 4 other markers on 20 linkage groups encompassing a genetic distance of 995 cM. These 2 pear maps were aligned using 37 co-dominant markers that showed segregating alleles in both parents. Out of 80 tested SSR markers developed from apple, more than four-fifth could produce discrete amplified fragments in pear. Thirty-eight apple SSR markers showed 39 segregating loci in the linkage map of 'Bartlett', while 27 markers produced 29 loci in 'Housui'. All pear linkage groups could be successfully aligned to the apple consensus map by at least 1 apple SSRs, suggesting that positions and linkages of SSR loci were well conserved between pear and apple. The self-incompatibility locus (S locus) was mapped to linkage group 17 in Japanese and European pears as well as apple. Our results are the first major effort in comparative mapping of pear and apple.