Abstract Complex hybridity is a rare diploid genetic system of plants, extensively characterized in Oenothera, in which heterozygosity for one or more reciprocal translocations is maintained by means of autogamy and a balanced lethal system. It is visible at metaphase I of meiosis as rings or chains of chromosomes held together by terminalized chiasmata. Phylogenetic analysis based on 274 random amplified polymorphic DNA markers showed that in the Australian endemic Isotoma petraea (Lobeliaceae) the genetic system had a single origin, as a ring-of-six, in the Pigeon Rock population. It subsequently spread to other populations to produce hybrids incorporating additional chromosomes into the rings. Our research supports the suggestion that complex hybridity is an evolutionary response to intense inbreeding and selected because it allows masking of accumulated deleterious alleles.