Landscape-level pollen, spore and charcoal particle analyses of four sites in southeastern New York State suggest the arrival of humans and megafaunal collapse occurred well in advance of the Younger Dryas climatic reversal. The distinctive spores of a dung fungus, Sporormiella, which serve as a proxy for megafaunal biomass, show a rapid decline at this time. A concomitant rise in stratigraphic charcoal indicates human transformation of the landscape also began many centuries before the return of boreal tree pollen, identified as a regional response to the Younger Dryas cooling event. An AMS date of 11,000±80 ¹⁴C yrbp on mastodon bone collagen from the Temple Hill site in Orange County is consistent with other late occurrences of extinct species regionally. A protracted extinction process is suggested in which an ecological collapse followed human arrival, but severely reduced populations of megafauna persisted until the end of the Pleistocene.