Tomato (Solanum lycopersicum) seed germination can be inhibited by continuous irradiation with far-red light (FRc) and re-induced by a subsequent red light pulse. In this study, we carried out a global transcript analysis of seeds subjected to FRc inhibitory treatment, with and without a subsequent red light pulse, using potato cDNA microarrays. We also identified and characterized genes involved in light-modulated germination as elements of the phytochrome signalling pathway. Microarray data showed that the inhibition of germination by FRc involves the induction of a large number of genes and the repression of a significantly smaller quantity. Multivariate analysis established an underlying pattern of expression dependent on physiological treatment and incubation time, and identified different groups of genes associated with dormancy maintenance, inhibition and promotion of germination. We showed that ELIP, CSN6, SOS2 and RBP are related to the photocontrol of germination. These genes are known to participate in other physiological processes, but their participation in germination has not been suggested previously. Light quality regulates the tomato seed transcriptome during phytochrome-modulated germination through changes in the expression of certain sets of genes. In addition, ELIP and GIGANTEA were confirmed as components of the phytochrome A signalling pathway during FRc inhibition of germination.