With the dye and medicinal plant Isatis indigotica (2n = 14) as pollen parent, intertribal sexual hybrids with Brassica napus (2n = 38, AACC) were obtained and characterized. Among a lot of F1 plants produced, only five hybrids (H1-H5) were distinguished morphologically from female B. napus parents by showing low fertility and some characters of I. indigotica, and also by having different chromosome numbers. H1-H4 had similar but variable chromosome numbers in their somatic and meiotic cells (2n = 25-30), and H5 had 2n = 19, the same number as the haploid of B. napus. GISH analysis of the cells from H1 and H5 detected one I. indigotica chromosome and one or two chromosome terminal fragments. New B. napus types with phenotypic and genomic alterations were produced by H1 after pollination by B. napus and selfing for several generations, and by H5 after selfing. A progeny plant (2n = 20) was derived from H1 after pollination by I. indigotica twice and had a phenotype similar to a certain type of B. rapa, showing that hybrid H1 likely retained all chromosomes of the A genome and lost some of the C genome in parental B. napus. The reasons for the formation of the partial hybrids with unexpected chromosomal complements and for the chromosome elimination are discussed.