A stratigraphic study of late Miocene–Pliocene mixed carbonate and siliciclastic sediment (upper part of the Yaque Group) was conducted in northern Hispaniola to refine the chronostratigraphy of uplifted, nearshore marine sequences in the Cibao Basin. Classic late Neogene sections in these sequences include a spectacularly preserved faunal record for the northern Caribbean. Refined ages of the Cercado Formation (6.6–6.0 Ma), the Gurabo Formation (ca. 5.8–4.0 Ma), and the Mao Formation (3.9–3.5 Ma) allow correlation to regional and global sea-level events. Each of the three formations corresponds to one depositional sequence, composed of mixtures, at different proportions, of skeletal debris, mostly coral, and mud-size (silt) siliciclastic sediment. Distinct stratal geometries and lithofacies individualize the three formations, each separated by pebble conglomerates. The Cercado Formation depositional sequence consists of prograding inner-shelf siliciclastic sands and patch reefs. The basal transgressive unit of the Gurabo Formation is made of seaward-prograding low-angle clinothems of bedded and burrowed siliciclastic sand with molluscs and free-living corals. The upper Gurabo unit consists of massive middle-shelf clinothems of silt with bedded reef debris and in situ branching coral thickets. These clinothems grade basinward into massive, deeper-water silt deposits at the shelf edge and basin slopes. The Mao Formation sequence records the transition from lowstand fluvial-deltaic facies to transgressive and highstand marine clinothems made mostly of coral debris in a silt matrix. In the Mao Formation outcrops, the coral-silt clinothems can be divided into at least 10 high-frequency cycles (40 k.y.?) based on lithofacies. Channelized and slumped coarse siliciclastic sand, gravel, and nonmarine alluvium cap the sequence, likely associated with lowered sea level starting at ca. 3.3 Ma and perhaps the onset of regional uplift. The major lithologic and sequence geometry changes in the Cibao Basin correlate with trends in the oxygen isotope ice-volume proxy and likely reflect deposition responding to major periods of marine transgression and highstand. An especially prominent feature is the major deepening and margin back step near the Miocene–Pliocene boundary, continuing in the early Pliocene, which resulted in the deposition of the Gurabo Formation. Transgression and sea-level highstand in the late–early Pliocene (3.9–3.5 Ma) produced distinctive margin progradation primarily by coral debris. This progradation event was synchronous with progradation in the nearby western Great Bahama Bank. The different stratal configurations of the three sequences can be attributed to a combination of factors, including: (1) shelf morphology and location on the shelf, (2) paleoceanographic conditions such as warm sea-surface temperatures and reduced upwelling, which controlled coral productivity and reef geometry, and (3) the influx of siliciclastic mud from the adjacent mountains.