Uncertainties in species definitions can have important consequences for biodiversity conservation because taxonomic rank is used as a criterion to assess the conservation priorities of threatened organisms. The Vulnerable St Lucia whiptail lizard Cnemidophorus vanzoi, considered a single species, is the sole representative of its genus in the Caribbean region, found on Maria Major and Maria Minor islands off the coast of St Lucia. However, a recent study revealed significant morphological and phylogenetic differences between the two populations and recommended they should be managed as two separate entities. We surveyed the two populations and estimated them to comprise 1,985 and 29 individuals on Maria Major and Minor, respectively. The Maria Minor population is currently at a critically low level and consequently highly susceptible to demographic and genetic stochasticity and catastrophic events, in particular the colonization of invasive mammalian predators. If our goal is to conserve biodiversity and evolutionary potential we face a dilemma in formulating the optimum strategy for the management of these two threatened populations on the species boundary. We discuss some potential management options but also raise this issue for discussion in the conservation biology community.