We apply a new approach for the delta C-13 analysis of single organic-walled microfossils (OWM) to three sites in the Appalachian Basin of New York (AB) that span the Late Devonian Biotic Crisis (LDBC). Our data provide new insights into the nature of the Frasnian-Famennian carbon cycle in the AB and also provide possible constraints on the paleoecology of enigmatic OWM ubiquitous in Paleozoic shale successions. The carbon isotope compositions of OWM are consistent with normal marine organic matter of autochthonous origins and range from -32 to -17 parts per thousand, but average -25 parts per thousand across all samples and are consistently C-13-enriched compared to bulk sediments (delta C-13(bulk)) by similar to 0-10 parts per thousand. We observe no difference between the delta C-13(OWM) of leiospheres (smooth-walled) and acanthomorphic (spinose) acritarch OWM, indicating that our data are driven by ecological rather than taxonomic signals. We hypothesize that the offset between delta C-13(OWM) and delta C-13(bulk) is in part due to a large delta C-13 gradient in the AB water column where OWM utilized relatively C-13-enriched dissolved inorganic carbon near the surface. Thus, the organisms producing the balance of the total organic carbon were assimilating C-13-depleted C sources, including but not limited to respired organic carbon or byproducts of fermentation. We also observe a systematic decrease in both delta C-13(OWM) and delta C-13(bulk) of 3 parts per thousand from shoreward to open-ocean facies that may reflect the effect of C-13-enriched dissolved inorganic carbon (DIC) derived from riverine sources in the relatively enclosed AB. The hypothesized steep carbon isotope gradient in the AB could be due to a strong biological pump; this in turn may have contributed to low oxygen bottom water conditions during the LDBC. This is the first time single-microfossil delta C-13(org) analyses of eukaryotes have been directly compared to bulk delta C-13(org) in the deep-time fossil record.