Chilling stress limits the early production of tomato, and can severely reduce the yield throughout the season. An advanced backcross population was developed using Lycopersicon esculentum E6203 and L. hirsutum LA 1777, a chilling tolerant accession. Sixteen plants from each of the 111 BC2S3 lines were grown at 25/18 C (day/night) for 5 weeks, and then exposed to 9/4 C in a growth chamber, under a photoperiod of 14 h and a light intensity of 400 μmol m-2 s-1 PPFD for 48 h. Chlorophyll fluorescence parameters were measured in situ before and after chilling, obtaining the variable to maximum fluorescence ratio (Fv/Fm), photochemical (qP) and non-photochemical quenching (qNP), and quantum efficiency of the photosystem II. These data were analyzed with the software qGene using a genetic map with 89 molecular markers. Two quantitative trait loci (QTL) were detected affecting qNP in chromosomes 1 and 6, and one QTL in chromosome 5, associated with both qP and Fv/Fm. Alleles from both species induced positive and negative effects. The effects of individual QTLs will have to be confirmed using near isogenic lines that contain a small introgression of the wild species genome into a cultivated tomato background.