The rare Tasmanian endemic Eucalyptus risdonii is thought to have arisen as a result of small, heterochronic changes to the genome of its more widespread sister species, E. tenuiramis. Previous morphological studies have shown that genetic differentiation between populations of E. risdonii and southern E. tenuiramis is continuous and much smaller than the separation between the southern and northern morphotypes of E. tenuiramis. However, morphological traits may be influenced by selection, possibly leading to convergence, requiring an independent measure of genetic variation. We studied allozyme frequency variation in E. risdonii, southern E. tenuiramis (parapatric with E. risdonii), northern E. tenuiramis (disjunct from southern populations), and E. coccifera (as an outgroup). Each morphotype had a level of genetic diversity close to the average reported in ten other eucalypt species with similar distributions but the coefficients of population differentiation within morphotypes were lower than in most other eucalypt species. The overall difference between morphotypes was extremely small, possibly as a result of recent and rapid differentiation, but may also be the result of gene flow from other peppermint taxa, including E. amygdalina and E. pulchella. Southern E. tenuiramis has greater genetic affinity with E. risdonii than with northern E. tenuiramis which supports recent evolutionary divergence of E. risdonii. In this study we have shown that taxonomic units are not necessarily aligned with an equitable partition of the gene pool and that conservation units should be much broader than single taxa in order to preserve evolutionary processes.