Expressed Sequence Tag (EST) analysis is a powerful means for evaluating gene expression and discovering novel genes. The method is relatively simple and particularly important for species where knowledge of the genome is unavailable or limited. In this study, we compare EST profiles of Emiliania huxleyi cultures grown under conditions that promote biomineralization and coccolithogenesis (F/50 media) and conditions that reduce these processes (F/2 media). A total of 3,527 clones from the F/50 and 4,116 clones from F/2 library were randomly selected and sequenced, resulting in a unigene set of 4,057 unique sequences comprised of 540 contigs and 3517 singletons. More than 40% of the expressed genes showed similarity to known genes from other organisms deposited in GenBank (e>10−2) and have been functionally categorized. The comparative data provide cues for further studies pertaining to genes and proteins involved in biomineralization and coccolithogenesis, and taken together serve as a valuable resource for the coccolithophorid research community.