With high-throughput Solexa sequencing technology,we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated,which were assembled into 31538 unigenes. Blast analysis showed that 56.7%unigenes were novel,which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered,including genes related to desiccation-(211) and high light-tolerance(31) ,flavonoid biosynthesis(10) ,reactive oxygen scavenging(48) and other stress-tolerance processes(208) ,which indicated there existed complex and diversity modes of stress tolerance in this species.A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway(except pyruvate phosphate dikinase) were discovered,which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra.Moreover,by statistically analyzing the types,proportions and frequencies of the interspersed repeats(TEs) and simple sequence repeats(SSRs) ,we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs,promoting our understanding of structural characteristics of the transcriptome.This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research. With high-throughput Solexa sequencing technology, we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated, which were assembled into 31538 unigenes. Blast analysis showed that 56.7% unigenes were novel, which Several hundreds of unigenes related to stress tolerance were discovered, including genes related to desiccation- (211) and high light-tolerance (31), flavonoid biosynthesis (10), reactive oxygen scavenging 48) and other stress-tolerance processes (208), which showed there existed complex and diversity modes of stress tolerance in this species. A complete set of essential genes involved in the C3- (57) and C4- (44) carbon fixation pathway (except pyruvate phosphate dikinase) were discovered, which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra. Moreover, by s tatistically analyzing the types, proportions and frequencies of the interspersed repeats (TEs) and simple sequence repeats (SSRs), we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs, promoting our understanding of structural characteristics of the transcriptome. this study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research.