Camelina (Camelina sativa L., Crantz) is an oilseed crop consisting of both spring- and winter-biotypes. Winter biotypes of camelina need a low-temperature treatment to acquire freezing tolerance and floral competence. However, spring biotypes do not require a low-temperature treatment to initiate flowering and do not cold acclimate to the same extent as winter biotypes. Exposure of the camelina winter biotype ‘Joelle’ to low temperature (5 °C) for 0-, 1-, 2-, 4-, and 6-weeks resulted in freezing survival rates of ~ 0%, 0%, 20%, 36%, and 72%, respectively, after being exposed to freezing conditions (−15 °C for 4 h). Winter biotype plants that survived the freezing treatment (42 d post-treatment under greenhouse conditions) also flowered; however, time to flowering was dependent on the cold treatment duration. Plants exposed to 5 °C for six weeks flowered first followed in order by plants exposed to 4- and 2-weeks cold. To decipher molecular regulation associated with low-temperature acquired freezing tolerance and floral competence in camelina, we analyzed the transcriptomes of a spring biotype (CO46) and winter biotype (Joelle) exposed to 0-, 1-, 2-, 4-, 6- and 8-weeks low temperature (5 °C). Genes and transcription factors with significant differential abundance (4-fold up or down) in the winter- compared to the spring-biotype of camelina were used to identify those over-represented among gene ontologies. The results highlighted gene ontologies associated with abiotic and biotic defense responses, oxidative stress responses, cell wall modification and cell expansion, biosynthesis of very long chain fatty acids and anthocyanins, as well as processes involving photosynthesis, sugar metabolism, transport, and phytohormone (abscisic acid, auxin, jasmonic acid, and salicylic acid) signaling. Transcripts associated with these processes in the winter biotype of camelina may be regulated by transcription factors similar to Arabidopsis MYB47, MYB75, MYB90, NF-YA4 and NF-YB2, HAT1, GRF7, CKG, and CBF1 and CBF2.