The Florida manatee (Trichechus manatus latirostris) is a protected species that is vulnerable to both anthropogenic and natural causes of mortality. The ability of wildlife managers to oversee regulation of this species is based on available abundance estimates and mortality data. Using existing manatee mortality data collected by Florida Fish and Wildlife Conservation Commission (FWC) from 1974-2012, this study focuses on identifying significant spatial clusters of high values or “hotspots” of manatee mortality and the temporal patterns of these hotspots using the novel “emerging hotspot analysis” ArcGIS tool. The categories of manatee mortality included in this analysis were watercraft-related, perinatal, cold-stress, and other natural (which includes red tide) and were classified into five hotspot pattern categories. Of interest were the locations where consecutive or new hotspot patterns were identified among the four categories of manatee mortality included in this analysis. Consecutive hotspot clusters were found near Tampa Bay (which includes parts of Pinellas, Hillsborough, and Manatee Counties) and in the counties of Hernando/Pasco, Monroe, Palm Beach/Broward/Miami-Dade, St. Johns/Flagler, and Citrus. New hotspot clusters were found in Tampa Bay (which includes parts of Pinellas, Hillsborough, and Manatee Counties) and in the counties of Nassau, Wakulla, Charlotte/Lee, St. Lucie/Martin, Levy, Duval, Dixie, Volusia/Seminole, and Citrus. These mortality hotspots frequently overlapped areas of higher manatee and human population densities. These hotspot clusters indicate emerging patterns that highlight areas to focus future research by wildlife managers; specifically, on the relationship between human population density and concentration of watercraft activities in coastal areas, as well as the influence coastal development has on the vital resources utilized by manatees.