The psychrophilic diatom Fragilariopsis cylindrus (Grunow) Krieger in Helmcke & Krieger was used to investigate photosynthesis and growth under freezing temperatures. Gene expression during a temperature shift from +5°C to -1.8°C was studied under 3 and 35µmol photons·m -2·s-1 by using a macroarray. These measurements were paralleled by determination of fluorescence induction at PSII and pigment analysis. The shift to - 1.8°C at 35µmol photons·m -2·s-1 caused a marginal decrease of photosynthetic quantum yield (Fv/Fm) from 0.61 to 0.52 with fast recovery after 1 day. The ratio of chl c to chl a increased from 3.1 to 5.5, and the ratio of diaioxanthin to diadinoxanthin increased from 0.7 to 5.0. Genes encoding proteins of PSII (psbA, psbC) and for carbon fixation (rbcL) were down-regulated, whereas genes encoding chaperons (hsp70) and genes for plastid protein synthesis and turnover (elongation factor EfTs, ribosomal protein rpS4, ftsH proiease) were up-regulated. In contrast, cold exposure at 3µmol photons· m-2·s-1 induced a marginal increase in Fv/Fm from 0.61 to 0.63 and a strong increase in fucoxanthin concentrations from 0.04 up to 0.12 pg·cell-1. This was paralleled by up-regulation of fcp genes. The ratio of chl c to chl a also increased from 3.1 to 4.2, as did the ratio of diatoxanthin to diadinoxanthin from 0.7 to 2.2. Down-regulation of psbA, psbC, and rbcL could also be measured but not up-regulation of hsp70, EfTs, rpS4, and the ftsH protease. The latter genes are probably necessary to avoid cold shock photoinhibition only at higher light intensities.