The genetic origin of many gold deposits, including Pogo in Alaska, remains controversial with questions as to whether they formed due to magmatic-hydrothermal or metamorphic-hydrothermal fluids. Gaining a better understanding of the formation mechanisms for these deposits is critical for defining proper exploration criteria in gold-bearing regions and production within these deposits. Monazite are light rare earth (LREE)-bearing and xenotime are heavy rare earth (HREE)-bearing phosphate minerals that are found as alteration products in many different gold deposits. In addition to their importance in geochronological investigations, their minor element chemistry may be used to differentiate between metamorphic, magmatic, diagenetic, and hydrothermal origin. This data release provides electron microprobe geochemical data that is used to showcase differences in these phosphates when derived from magmatic-hydrothermal systems compared to metamorphic-hydrothermal systems. The electron microprobe data was collected by personnel of the Central Region Minerals Program in Denver, Colorado, for the U.S. Geological Survey (USGS) Mineral Resources Program (MRP). Appreciable differences in chemistry were noted for deposits associated with alkaline magmatic systems (Taurus, AK, and Cripple Creek, CO), calc-alkaline magmatic systems (Pebble, AK, and Butte, MT), and orogenic gold systems derived from metamorphic-hydrothermal systems (systems from Grass Valley, the Mother Lode, and the Klamath Mountains in CA). These characteristics were then applied to the controversially classified Pogo gold deposit, Alaska, in order to provide evidence for how it formed.