 The study aimed to generate enormous transcript sequences from sweet potato root using high-throughput transcriptome sequencing technology. A total of 59 million sequencing reads were generated, yielding 56,516 unigenes with an average length of 581 BP out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway Database, KEGG, indicated that 17,598,31.14% unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways. Additionally, 4,114 cDNA SSRs, CSSRs, were identified as potential molecular markers in the study. 100 pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests. These sequences and markers will provide valuable resources for the sweet potato community, and transcriptome analysis based on Illumina paired end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species.