Cynara cardunculus L. (2n=2x=34) includes three botanical taxa: the globe artichoke (var. scolymus L.), the cultivated cardoon (var. altilis DC), and their wild progenitor, the wild cardoon [var. sylvestris (Lamk) Fiori]. Italy is the world's leading producer of globe artichoke, while the cultivated cardoon is grown mainly in Southern Europe for comestible purposes, although it also has been proposed as a source of both biomass and biodiesel. The most saturated genetic map has been recently developed from a set of F1 progeny of a cross between a globe artichoke and a cultivated cardoon genotypes, using a two-way pseudo-testcross strategy. Most of the ~1,000 informative markers, including a set of 172 EST-SSR loci (developed within the Compositae Genome Project), were integrated into the reference C. cardunculus genetic maps, wide covering the 17 linkage groups. Transcriptome sequencing for three parental genotypes was carried out using 454 technology. This approach generated some 1.7M reads assembled into 38,726 reference transcripts, which were annotated by gene ontology terms via Blast and InterPro analyses. Putative enzyme coding sequences were tagged using KEGG database. Transcription factor activity was assigned to 1,398 transcripts, while 316 sequences were identified as candidate resistance genes. Sequencing of cDNA from further eight C. cardunculus accessions was carried out with Illumina GAII. Paired-end reads (46M, 6.9Gbp) were aligned on reference transcripts together with 454 reads. Overall, 195,400 candidate SNPs were called using a Bayesian method (posterior probability > 95%) and a validation rate of 90% was reported by Sanger sequencing.