Fossilized leaf mines and other traces of phytophagous insects provide a unique window into ecological and evolutionary associations of the past. Leaf-mining flies (Diptera: Agromyzidae) are an important component of the recent leaf-mining fauna, but their fossil record is sparse compared to other mining insect lineages; many putative agromyzid body fossils and traces are dubiously assigned. Agromyzid leaf mines often can be distinguished from those of other insects by the presence of an intermittent, fluidized frass trail that may alternate between the sides of the mine. Here, we describe two new Paleogene leaf mine fossils, Phytomyzites biliapchaensis Winkler, Labandeira and Wilf n. sp. from the early Paleocene of southeastern Montana, USA, occurring in leaves of Platanus raynoldsii (Platanaceae); and Phytomyzites schaarschmidti Wappler n. sp., from the middle Eocene of Messel, Germany, occurring in leaves of Toddalia ovata (Rutaceae). These fossils both exhibit frass trails indicative of an agromyzid origin, and P. biliapchaensis also exhibits associated stereotypical marks identical to damage caused by feeding punctures of extant adult female Agromyzidae prior to oviposition. Phytomyzites biliapchaensis represents the earliest confirmed record of Agromyzidae, and one of the earliest records for the large dipteran clade Schizophora. Plant hosts of both species belong to genera that are no longer hosts of leaf-mining Agromyzidae, suggesting a complex and dynamic history of early host-plant associations and, for the early Paleocene example, an evolutionary, possibly opportunistic colonization in the midst of the ecological chaos following the end-Cretaceous event in North America.