Abstract The Middle Devonian Geneseo Formation and its lateral equivalents in the Northern Appalachian Basin are regarded as crucial secondary targets to the extensively explored Marcellus subgroup. High-resolution sedimentology, stratigraphy, and petrography have yielded differentiation of genetically related packages, comprised of distinct lithofacies with characteristic physical, biological, and chemical attributes. In addition, argon ion milling and nanoscale scanning electron microscopy of shale sections has shown that the pore structure of the Geneseo derives from pores defined by phyllosilicate frameworks, carbonate dissolution, and within organic matter. Intervals of silt-rich mudstones and muddy siltstones occur in multiple facies types and “interrupt” facies, reflecting background sedimentation. These deposits and their sedimentary features are interpreted as products of high-density fluvial discharge events. Pore morphology and distribution correlates with distinct mudstone lithofacies as a result of small-scale compositional and textural characteristics. Phyllosilicate framework pores are small triangular openings (100-1500 nm wide) and are the dominant pore type observed in hyperpycnites. Organic matter porosity is common (10-500 nm pore size) and dominates the organic-rich facies that represents “background” sedimentation with high organic content. Carbonate dissolution pores (50-500 nm wide) are observed in calcareous intervals and reflect partial dissolution of carbonate grains during catagenetic formation of carboxylic/phenolic acids.