We have examined the Neogene stratigraphic successions recovered from six wells located along a present-day middle neritic (current depositional depth 92 m) to upper bathyal depth (current depositional depth 482 m) transect oblique to the shelf/slope margin in the northern Gulf of Mexico (GOM) using calcareous plankton biostratigraphy. The latter were used to conduct stratigraphic interpretation of the sections and to determine their completeness. We establish that all sections vary considerably in thickness and completeness, depending on depth of deposition, as estimated from benthic foraminiferal analysis, which shows that depositional depth at the six sites changed little through the Neogene. The shallowest section (~90-m estimated depositional depth through the Neogene) is the thinnest with the most complete Upper Miocene–Pleistocene record, whereas the deepest section (~600– 800-m estimated depositional depth) is the thickest but also contains the least complete Pliocene–Pleistocene record. The Upper Miocene to Pleistocene sediments deposited between ~200- and 500-m estimated depositional depth exhibit a characteristic allostratigraphic architecture, with sedimentary units bounded by unconformities associated with 1- to 2-Myr hiatuses that vary little along the transect. We integrate the stratigraphic architecture along our local transect in the regional Cenozoic depositional framework in the GOM of Galloway and coauthors and establish that the allostratigraphic units (AUs) correspond well with several of the genetic and seismic sequences delineated. We interpret the depth-related increase in thickness of the Upper Miocene–Pleistocene AUs in light of the sedimentary processes discussed by these authors. However, our interpretation differs considerably from theirs based on our documentation of temporally incomplete sections in the wells. The sedimentary pattern in Well-3 (~200-m estimated depositional depth) is quite different from that at nearby Well-1 (~100–600-m estimated depositional depth), although very similar to the wells further west, even though the distance between Well-3 and Well-6 is about four times that between Well-3 and Well-1. We note also that the stratigraphic pattern in Well-1 changed ~8 Ma, from highly discontinuous before to remarkably continuous after. We have found no clear evidence that glacio-eustasy shaped the Neogene stratigraphic record in the study area. Therefore, we question whether glacio-eustasy was the primary forcing mechanism on stratigraphic architecture in the GOM beyond the shallow part of shelves and propose that salt tectonics may have been a more prominent factor in controlling accommodation. An allostratigraphic architecture was described earlier from the De Soto Canyon northeast of the GOM transect, where the AUs and their boundaries were shown to match, respectively, the seismic sequences and surfaces on the nearby Florida margin. We therefore consider the AUs along the GOM transect as corresponding as well to seismic sequences and therefore to parts of depositional sequences. Based on this, we review notable difficulties in characterizing seismic features (sequences and surfaces) in concrete stratigraphic records and recommend a greater awareness of the temporal significance of unconformities, many of which are associated with multimillion-year hiatuses.