Prehistoric passenger pigeon bones have been found at many sites in New York. The Hiscock site in Genesee County has a single passenger pigeon bone from a Late Pleistocene context and at least 292 pigeon bones from Holocene levels. Dutchess Quarry Cave No. 1 in Orange County has several Ectopistes bones from Holocene contexts including five from Stratum 1 and two from Stratum 2. The nearby Dutchess Quarry Cave No. 8 has two pigeon bones from an Early Holocene context (c. 11,000 to 5,800 years ago). At the Rabuilt Cave (PKE 4-1) site, also in Dutchess County, two passenger pigeon bones dating from the Middle to Late Archaic period were identified. All these are sites where many, if not most, of the faunal remains were likely accumulated by natural means, rather than human hunting.
Passenger pigeon bones become more common in Late Archaic sites, although relatively few excavated sites of this time period contain large numbers of any kind of animal bones. At the Lamoka Lake site in Schuyler County, passenger pigeon is abundant. At the Cole Gravel Pit site in Livingston County, which dates to about 3,900 B.P., over 400 bones were identified as passenger pigeon.
Large numbers of passenger pigeon bones have been identified at several other New York sites, including the the c. A.D. 1200 Oakfield Site (Mda 1-4) in Genesee County, Contact Period (late seventeenth century) Weston and Indian Hill sites in Onondaga County, and the Indian Castle and Spaulding Lake sites. At the Tram Site, one human burial contained a more or less complete pigeon skeleton under a ceramic pot. Pigeons were also found associated with two burials at the Cameron site. Both of these are Early Contact Seneca sites.