Abraham Halsey published the first checklist of New York City lichens in 1823. It was the first work focused on lichens in North America. Study of this baseline—among the oldest, most comprehensive outside of Europe—has been complicated because the supporting vouchers were believed destroyed in an 1866 fire that consumed the collections of the New York Lyceum, predecessor of the New York Academy of Sciences. The discovery of Halsey's collection in the Brooklyn Botanic Garden herbarium is reported here. The history and contents of the collection are discussed in detail, updated identifications are provided for all specimens, Halsey's checklist is updated to modern taxonomic concepts, and the 1823 baseline is compared to the present day. The collection contains 265 specimens, 126 of which are vouchers that correspond to 114 of the 190 names from his published checklist. An additional 88 specimens appear to be post-1823 collections from New York made by Halsey. In total, Halsey's New York City specimens correspond to 129 species, of which only 18 now occur in the region. Shifts in the lichen biota of New York City, occurring after near-complete extirpation in the 1960s, followed by subsequent recolonization, demonstrate modern trends toward lower foliose and fruticose lichen diversity, lower diversity of sexually reproducing taxa, and lower diversity of taxa that associate with ecologically restricted photobionts such as Trentepohlia and cyanobacteria. The historical lichen communities of the area resembled those of existing remnant mature and old-growth high-quality habitats in the Central Appalachian Mountains and Mid-Atlantic Coastal Plain. It is shown that the authorship of the eight new taxa described in the 1823 checklist should be attributed to Halsey, and the taxonomic identity of each taxon is discussed in detail. Cetraria viridis (≡ Vulpicida viridis) is lectotypified and the prior neotype overturned, Lecidea versicolor is neotypified and placed in synonymy with Xanthosyne varians, Pyrenula enteroleuca is lectotypified and placed in synonymy with Conotrema urceolatum, Verrucaria composita is lectotypified, transferred to Viridothelium as V. compositum, and the common V. virens is placed in synonymy and lectotypified. The original material of Spiloma roseum Halsey nom. illeg. is shown to be conspecific with Coniarthonia pyrrhula. The identities of Lecanora juglandina and Lecanora irregularis remain unresolved. This study resurrects the legacy of a pioneering naturalist whose work came to be reduced to a lichenological footnote and whose role in New York City botany has been largely forgotten. This study also highlights the value of natural history collections in reconstructing historical ecosystems, contextualizing centuries of human-mediated environmental change, and informing conservation. It illustrates the wealth of irreplaceable information in New York State botanical collections, and the urgent need to assure that these are preserved, digitized, and most importantly, continuously restudied. Importantly, archival records newly reported on here unequivocally dispute the historical narrative that the herbarium of the New York Lyceum was destroyed by fire and instead suggest it survived in the Mercantile Library Association at Astor Place in Manhattan. The present-day whereabouts of this invaluable herbarium are unknown, and it is likely unnoticed and unrecognized in an institutional library or archive somewhere in the New York City metropolitan region.