To elucidate the molecular basis of cold acclimation in strawberry (Fragaria x anannassa), we have begun studies to identify genes associated with low temperature (LT) acclimation. Differential screening of a cDNA library prepared from cold-acclimated strawberry plants allowed us to isolate several cDNAs showing differential expression at LT. Northern analysis showed that the transcript level of Fcor1 (Fragaria Cold-Regulated) peaked after 2 days of LT exposure while that of Fcor2 peaked after 2 weeks. On the other hand, the level of Fcor3 transcript decreased within 24 hours of LT exposure and remained low during the 8 weeks acclimation period. Fcor1 and Fcor2 are expressed in all tissues while Fcor3 is specific to leaves. The Fcor1-encoded protein has a compositional bias for leucine, isoleucine, glycine, proline and serine. This protein shares homology with the proteins encoded by blt101, a LT-responsive gene from barley, and ESI3, a gene induced by salt stress in Lophopyrum. The FCOR2 protein is rich in lysine, leucine, valine, alanine and arginine, and shows no homology with any known gene products. The partial Fcor3 cDNA clone encodes a polypeptide that shows a very high identity with the spinach PSI subunit V and with the PSI PsaG polypeptide from barley. The level of Fcor1 transcript accumulation is correlated with the freezing tolerance of the strawberry cultivars used in our study. This suggests that Fcor1 may be useful as a molecular marker to select for this trait in resulted species of the Rosaceae family.