The existence of coral reef ecosystems relies critically on the mutualistic relationship between calcifying cnidarians and photosynthetic, dinoflagellate endosymbionts in the genus Symbiodinium. Reef-corals have declined globally due to anthropogenic stressors, for example, rising sea-surface temperatures and pollution that often disrupt these symbiotic relationships (known as coral bleaching), exacerbating mass mortality and the spread of disease. This threatens one of the most biodiverse marine ecosystems providing habitats to millions of species and supporting an estimated 500 million people globally (Hoegh-Guldberg et al. 2007). Our understanding of cnidarian–dinoflagellate symbioses has improved notably with the recent application of genomic and transcriptomic tools (e.g. Voolstra et al. 2009; Bayer et al. 2012; Davy et al. 2012), but a model system that allows for easy manipulation in a laboratory environment is needed to decipher underlying cellular mechanisms important to the functioning of these symbioses. To this end, the sea anemone Aiptasia, otherwise known as a ‘pest’ to aquarium hobbyists, is emerging as such a model system (Schoenberg & Trench 1980; Sunagawa et al. 2009; Lehnert et al. 2012). Aiptasia is easy to grow in culture and, in contrast to its stony relatives, can be maintained aposymbiotically (i.e. dinoflagellate free) with regular feeding. However, we lack basic information on the natural distribution and genetic diversity of these anemones and their endosymbiotic dinoflagellates. These data are essential for placing the significance of this model system into an ecological context. In this issue of Molecular Ecology, Thornhill et al. (2013) are the first to present genetic evidence on the global distribution, diversity and population structure of Aiptasia and its associated Symbiodinium spp. By integrating analyses of the host and symbiont, this research concludes that the current Aitpasia taxonomy probably needs revision and that two distinct Aiptasia lineages are prevalent that have probably been spread through human activity. One lineage engages in a specific symbiosis with Symbiodinium minutum throughout the tropics, whereas a second, local Aiptasia sp. population in Florida appears more flexible in partnering with more than one symbiont. The existence of symbiont-specific and symbiont-flexible Aiptasia lineages can greatly complement laboratory-based experiments looking into mechanisms of symbiont selectivity. In a broader context, the study by Thornhill et al. (2013) should inspire more studies to target the natural environment of model systems in a global context targeting all participating member species when establishing ecological and genetic baselines.