Explaining the origin and maintenance of phenotypic variation remains a central challenge in evolutionary biology. Using the trematode parasite Maritrema novaezealandensis, we examined variability in several morphological, behavioural, and physiological phenotypic traits at the same time as controlling for genotype by using genetically identical parasite clonal lineages. We measured several morphological traits, photoreactive responses, and survivorship to quantify the amount of phenotypic variation within and among 42 clonal parasite lines. Additionally, we tested Lerner's hypothesis that homozygotes are more variable than heterozygotes and assessed correlations between heterozygosity and phenotypic variation among clones. We found substantial differences among clones in morphology, photoreactive behaviour, and survivorship, yet no significant differences among clones in levels of intraclonal phenotypic variability were seen. Although the results demonstrate that conspecific trematode clones have significantly different levels of phenotypic variability, consistent differences over time were not always apparent. Finally, no correlation was found between heterozygosity and phenotypic variation among clones and the pattern of highly variable homozygotes, as observed by Lerner, was not evident in the present study. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103, 106–116.