The transcriptome of Kappaphycus alvarezii was profiled using high-throughput Solexa paired-end sequencing technology. A total of 61 million sequencing reads was generated by filtering the low-quality reads, and 28 701 unigenes with a mean length of 901 bp were obtained based on de novo assembly. In similarity alignments against the NCBI non-redundant protein sequence (NR) database, Swissprot database, Cluster of Orthologous Groups (COG) database, Gene ontology (GO) database, and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 11 996 (41.79%) unigenes were identified with significant hits (E-value < 10(-5)) against existing genes. Functional annotation with the KEGG pathway database identified 8975 unigenes and mapped to 125 pathways. Through functional enrichment analysis of the genes with a higher expression value than the average RPKM (reads per kilobase per million reads), we found that some important pathways were highly expressed. The substantial number of transcript sequences of K. alvarezii provides a valuable resource for potential gene identification and comparative genomic studies.