The PM687 line of Capsicum annuum L. has a single dominant gene, Me-3, that confers heat-stable resistance to root-knot nematodes (RKN). Me-3 was mapped using doubled-haploid (DH) lines and F-2 progeny from a cross between the susceptible cultivar 'Yolo Wonder' ('YW') and the highly resistant line 'PM687'. Bulked-segregant analysis with DNA pools, from susceptible or resistant DH lines, was performed to identify RAPD and AFLP markers linked to Me-3. There was no polymorphism between bulks of ten DH lines using over 800 RADP primers (4,000 amplified fragments analysed). Using 512 AFLP primers (74,000 amplified fragments analysed), and bulked DNA templates from 20 resistant and 20 susceptible plants, we identified eight repulsion-phase and four coupling-phase markers linked to Me-3. Analysed in 103 DH progeny, they defined a 56.1-cM interval containing the target gene. The nearest were located 0.5, 1.0, 1.5 and 3.0 centimorgans (cM) on both sides of the gene. Analysis of the F-2 progeny (162 plants) with the nearest coupling-phase marker confirmed its close position. Another resistance gene to RKN, present in 'PM687' (Me-4), was shown to be linked to Me-3, 10 cM from it. In order to localize Me-3 and Me-4 on our reference intraspecific pepper linkage map, two AFLP markers were mapped. The Me-3 nearest marker was 10,1 cM from a RAPD marker named Q04_0.3 and 2.7 cM from a RFLP marker named CT135. We investigated map-position orthologies between Me-3 and two other nematode resistance genes, the tomato Mi-3 and the potato Gpa(2) genes, which mapped in the telomeric region of the short arm of the tomato and potato chromosome 12 (or XII for potato).