We build a stylized model to gain insights into the application of conservation payments to protect endangered species in the face of wildlife-livestock disease risks and habitat fragmentation. Greater connectivity of habitat creates an endogenous trade-off. More connectedness ups the chance that populations of endangered species will grow more rapidly; however, greater connectivity also increases the likelihood that diseases will spread more quickly. We analyze subsidies for both habitat connectedness and livestock vaccination. We find the cost-effective policy is to initially subsidize habitat connectivity rather than vaccinations; this increases habitat contiguousness, which eventually also increases disease risks. Once habitat is sufficiently connected, disease risks increase to such a degree to make a vaccination subsidy worthwhile. Highly connected habitat requires nearly all the government budget be devoted to vaccination subsidies. The result of the conservation payments is significantly increased species abundance, for a wide range of initial levels of habitat connectedness.