To analyze inheritance and presence of donor DNA from Eruca sativa in progenies derived from somatic hybrids between Eruca sativa Brassica napus, two E. sativa specific repetitive DNA sequences were isolated and characterized by DNA sequencing. One of the sequences, ESR64, showed 100% similarity with a part of the E. sativa rDNA intergenic spacer. In situ hybridization to metaphase chromosomes of E. sativa revealed six sites of hybridization, indicating that E. sativa has three rDNA loci. The other clone, ESR92, was shown to be a tandemly repeated element located close to the telomeres on at least ten chromosomes. Analysis of progenies derived from the somatic hybrids, using these two repetitive sequences as probes, revealed the presence of E. sativa DNA. Furthermore, cytogenetic analyses with genomic in situ hybridization (GISH), was performed, using differently labelled total DNA from the two parental species, in combination with a preannealing step to remove common sequences. These experiments showed that labelling in B. napus was restricted to the centromeric regions while a uniform distribution over the chromosomes was found in E. sativa. With the GISH technique it was also revealed that the somatic hybrid progeny contained one or two complete E. sativa chromosomes, but no intergenomic translocations could be detected.