Plant resistance genes interacting specifically with pathogen avirulence genes provide a unique opportunity to test the hypothesis that coevolution of a host and its parasites (including pathogens) provides an advantage to sexual reproduction. Here, we determined candidate resistance genes of Japanese dandelion Taraxacum japonicum as a step to test the advantage of sex. T. japonicum is known to be hybridizing with asexual European dandelion T. officinale naturalized in Japan. First, nine individuals of T. japonicum, three each from Tokyo, Aichi, Fukuoka, were collected in the field. We extracted RNA from leaves, synthesized cDNA, and determined those sequences by a Next Generation Sequencer 454 FLX-ti. The 1,576,593 short-reads were assembled using Newbler into 39,904 contigs. These contigs were searched its homolog using BLAST (blastn, tblastx) against R-genes from Lactuca saliva and T. oficinale. A total of 226 contigs were closest hits (1xe^-20 threshold). Then, these 226 contigs were further selected using a criterion of BLAST (blastx) hits (1xe^-10 threshold) to the reference protein sequence of Arabidopsis thaliana. A total of 155 contigs were closest hits and are considered candidate resistance genes in T. japonicum. Our study showed that cDNA sequencing with Next Generation Sequencer is very effective to determine candidate resistance genes of wild plants.