Abstract Background The sequenced genomes of cucumber, melon and watermelon have relatively few R -genes, with 70, 75 and 55 copies only, respectively. The mechanism for low copy number of R -genes in Cucurbitaceae genomes remains unknown. Results Manual annotation of R -genes in the sequenced genomes of Cucurbitaceae species showed that approximately half of them are pseudogenes. Comparative analysis of R -genes showed frequent loss of R -gene loci in different Cucurbitaceae species. Phylogenetic analysis, data mining and PCR cloning using degenerate primers indicated that Cucurbitaceae has limited number of R -gene lineages (subfamilies). Comparison between R -genes from Cucurbitaceae and those from poplar and soybean suggested frequent loss of R -gene lineages in Cucurbitaceae. Furthermore, the average number of R -genes per lineage in Cucurbitaceae species is approximately 1/3 that in soybean or poplar. Therefore, both loss of lineages and deficient duplications in extant lineages accounted for the low copy number of R -genes in Cucurbitaceae. No extensive chimeras of R -genes were found in any of the sequenced Cucurbitaceae genomes. Nevertheless, one lineage of R -genes from Trichosanthes kirilowii , a wild Cucurbitaceae species, exhibits chimeric structures caused by gene conversions, and may contain a large number of distinct R -genes in natural populations. Conclusions Cucurbitaceae species have limited number of R -gene lineages and each genome harbors relatively few R -genes. The scarcity of R -genes in Cucurbitaceae species was due to frequent loss of R -gene lineages and infrequent duplications in extant lineages. The evolutionary mechanisms for large variation of copy number of R -genes in different plant species were discussed.