New methods of genomic analysis are greatly improving our ability to learn about animals and to mitigate threats against them. I provide examples from my research program illustrating the use of genome analysis, DNA capture, metabarcoding, and transcriptomics in a range of studies dealing with endangered animal species. These include, among others, studies of amphibians threatened with invasive chytrid fungus, native Hawaiian birds surviving introduced avian malaria, the role of ship ballast water in spreading invasive pathogens around the world, and the use of next generation sequencing methods to assess genetic structure in salamanders, Hawaiian birds, and island foxes.