While the population of endangered whooping cranes (Grus americana) has grown from 15 individuals in 1941 to an estimated 304 birds today, the population growth is not sufficient to support a down listing of the species to threatened status. The degree to which disease may be limiting the population growth of whooping cranes is unknown. This conservation medicine project described selected parasites of potential concern infecting the only self-sustaining wild population of whooping cranes. Using a non-invasive sampling approach, we assessed the prevalence and phenology of Eimeria oocysts in whooping crane fecal samples collected across two winter seasons (November 2012 – April 2014) at the Aransas National Wildlife Refuge along the Texas Gulf coast, USA. Across both years, 26.5% (n=328) of fecal samples were positive for Eimeria based on microscopy, and 16.4% (n=262) of samples were positive by PCR; phylogenetic analyses confirmed the infection with Eimeria gruis and E. reichenowi, two species known to produce disseminated visceral coccidiosis and high juvenile mortality in captive cranes. In addition, we obtained blood samples from these cranes to screen for several vector-borne hemoparasites via PCR. We documented Plasmodium,or Haemoproteus infections in 62% (n=61) of blood samples, and Leucocytozoon infections in 7%. The phylogenetic analysis revealed that most sequences for each Plasmodium lineage were identical to each other and formed a unique clade distinct from previously published sequences. Taken together, these results suggest that birds are being exposed to these pathogens prior to arriving on the wintering grounds in Texas. Understanding the epidemiology of coccidiosis and vector-borne pathogens, which are capable of regulating host populations, are important for management efforts to increase population growth of the endangered whooping crane.