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Coupled hurricane–ocean forecast models require proper initialization of the ocean thermal structure. Here, a new feature-based (F-B) ocean initialization procedure in the GFDL/University of Rhode Island (URI) coupled hurricane prediction system is presented to account for spatial and temporal variability of mesoscale oceanic features in the Gulf of Mexico, including the Loop Current (LC), Loop Current eddies [i.e., warm-core rings (WCRs)], and cold-core rings (CCRs). Using only near-real-time satellite altimetry for the “SHA-assimilated” case, the LC, a single WCR, and a single CCR are assimilated into NAVOCEANO’s Global Digitized Environmental Model (GDEM) ocean temperature and salinity climatology along with satellite-derived daily sea surface temperature (SST) data from 15 September 2005 to produce a more realistic three-dimensional temperature field valid on the model initialization date (15 September 2005). For the “fully assimilated” case, both near-real-time altimetry and real-time in situ airborne XBT (AXBT) temperature profiles are assimilated into GDEM along with SST to produce the three-dimensional temperature field. Vertical profiles from the resulting SHA-assimilated and fully assimilated temperature fields are compared to 18 real-time AXBT temperature profiles, the ocean climatology (GDEM), and an alternative data-assimilated product [the daily North and Equatorial Atlantic Ocean Prediction System Best Estimate (RSMAS HYCOM), which uses an Optimal Interpolation (OI) based assimilation technique] to determine the relative accuracy of the F-B initialization procedure presented here. Also, the tropical cyclone heat potential (TCHP) from each of these profiles is calculated by integrating the oceanic heat content from the surface to the depth of the 26°C isotherm. Assuming the AXBT profiles are truth, the TCHP rms error for the F-B SHA-assimilated case, the F-B fully assimilated case, the GDEM ocean climatology, and the RSMAS HYCOM product is 12, 10, 45, and 26 kJ cm−2, respectively.