The genetic relationships between and within Hibiscus syriacus, Hibiscus sinosyriacus and Hibiscus paramutabilis, three winter hardy Hibiscus species native to China, were analysed by the amplified fragment length polymorphisms (AFLP) technique and by morphological evaluation of flower and leaf characteristics. Both methods clearly discriminated between the three species. H. sinosyriacus was classified as an intermediate form between H. paramutabilis and H. syriacus; however, it showed a higher similarity to H. paramutabilis. The different H. syriacus cultivars could be identified by AFLP analysis, while also leaf indices clustered the different cultivars in small groups. Flow cytometry showed that both triploid and tetraploid cultivars occur in the H. syriacus assortment. In general triploid cultivars had larger flowers compared to diploid cultivars.