A detailed, genetic stratigraphic framework for paleoceanographic studies can be derived by describing, correlating, interpreting, and predicting stratigraphic sequences relative to a hierarchy of their constituent time-stratigraphic transgressive-regressive units (“T-R units”). T-R unit hierarchies are defined and correlated using lithostratigraphic and paleoecologic data, but correlations can be enhanced or “checked” (tested to confirm or deny) with objective biostratigraphic, magnetostratigraphic, or chemostratigraphic data. Such chronostratigraphies can then be bracketed by radiometric ages, so that average periodicities for T-R units can be calculated and a hierarchal geochronology derived. T-R units are inferred to be the net depositional result of eustatic cycles of sea level change and can be differentiated from autocyclic deepening-shallowing units because the latter are noncorrelative intrabasinally. Boundaries between T-R units are conformable or unconformable “genetic surfaces” of two types: transgressive surfaces and “climate change surfaces”. The latter are useful for correlating minor transgressive phases through nonmarine intervals, thereby deriving information linking paleoclimatic and paleoceanographic processes. Permo-Carboniferous sequences can be analyzed relative to a hierarchy of six scales of genetic T-R units having periodicities of 225–300 m.y. (first order), 20–90 m.y. (second order), 7–13 m.y. (third-order), 0.6–3.6 m.y. (fourth order), 300–500 × 10³ years (fifth order), and 50–130 × 10³ years or less (sixth-order). Paleogeographic maps for the time of maximum transgression (“transgressive apex”) of successive fifth-order T-R units (5–25 m thick) in the Glenshaw Formation (Upper Pennsylvanian, Northern Appalachian Basin) delineate delta lobes, embayments, islands, and linear seaways. Relative extent of marine inundation on the fifth-order maps was used to delineate fourth-order T-R units, and the fourth-order T-R units constitute the transgressive half of a third-order T-R unit. This third-, fourth-, and fifth-order hierarchy is correlated more than 1200 km (750 miles) to the Western Interior “Basin,” and is confirmed with limited objective biostratigraphy.