Scytosiphon lomentaria (Lyngbye) Link is a species of brown algae common in the eulittoral and sublittoral zones of temperate oceans. Some populations exhibit an asexual heteromorphic life cycle that is regulated by photoperiod. While this response is mediated by blue light, virtually nothing is known regarding downstream genes that are activated or repressed during photo-morphogenesis in this organism. This study examined photoperiodic mediation of differential gene expression in S. lomentaria using isolates obtained from the eastern coast of Virginia, USA. Putative differentially expressed transcripts were produced by differential display reverse transcriptase polymerase chain reaction (PCR), cloned and sequenced. The sequences where identified using bioinformatics tools, and the expression patterns analyzed and validated by quantitative Real-Time PCR. Of the 133 putative differentially expressed bands selected, 92 were successfully sequenced and analyzed. Of these, 27 could not be matched to known sequences. Twenty-eight transcripts were found to have high similarity to sequences in the databases and transcript levels were quantified. Seventeen were upregulated under a short day, one was downregulated, five showed no expression differences, four did not amplify and one was the reference gene. These analyses provide new insights into the genetic response to photoperiod-mediated morphogenesis in S. lomentaria.