R. raciborskii is known for growing under wide ranges of temperature and light. In temperate regions, however, low temperature and high light may serve as a stressful condition for invading tropical populations. The genetic basis of R. raciborskii's adaptation to this combination of stresses are unknown. In this study, the growth rate and the expression of genes that may be crucial in the response to the chill/light stress of two R. raciborskii strains (differing in their climatic origin and toxicity) exposed to low temperature and high light were examined. Results showed that AMU-DH-30, a non CYN (cylindrospermopsin) producing strain isolated from the temperate region, exhibited under stress the upregulation of genes involved in the protein translation (rbp1, nusG, hflX), membrane fluidity (desA), photosynthetic activity (ccr2 and ftsH), and the accumulation of compatible solutes (asd). In contrast, a CYN producing Australian strain CS-505 was not able to adapt quickly and to continue growth during stress conditions. Intriguingly, CS-505 and AMU-DH-30 had a similar ability to resume growth when the stress conditions subsided. Moreover, in strain CS-505 the cyrB gene was significantly upregulated under the stress conditions. The presented results shed new light on the possible mechanisms involved in the response of R. raciborskii to chill/light stress.