The first open ocean deployment of the Skin Depth Experimental Profiler (SkinDeEP) was from the R/V Melville in the Gulf of California during the Marine Optical Characterization Experiment (MOCE-5). SkinDeEP is an autonomous, vertical profiler for the upper few meters of the ocean. During MOCE-5, SkinDeEP was deployed on ten separate occasions, and profiles were made at intervals of approximately 1 min each. A total of 976 profiles was acquired during the cruise. The ocean skin temperatures were measured by the Marine Atmosphere Emitted Radiance Interferometer (M-AERI), an infrared spectroradiometer. Typical meteorological conditions were of low winds and high insolation. The data set provided captures the near-surface temperature structure that decouples the skin layer from the conventional in situ bulk sea surface temperature (SST) measurements made at a depth of a few meters. Data from SkinDeEP showed strong diurnal warming within the upper few meters, with one extreme case of 4.6 K. There were large discrepancies when computing the skin-bulk temperature difference with bulk temperatures at different depths. Results also show the strong dependency of the SST on air-sea heat flux estimates, with warm-layer errors of almost 60 Wm-2 associated with intense stratification. This indicates the importance of the inclusion of the skin temperature for accurate calculation of latent, sensible, and net longwave heat fluxes.