Ichnofabric analysis was conducted in Miocene sediments from Lepe (Huelva, SW Spain) based on integrative outcrop and core research, to improve interpretations of depositional and paleoenvironmental conditions, with special attention to sequence stratigraphy. Seven intervals were differentiated in outcrops based on stratigraphic and ichnological features, consisting of two ichnofabrics: Ophiomorpha-Thalassinoides-Spongeliomorpha ichnofabric characterizes intervals 1, 2, 6, 7 and 8, while Palaeophycus-Planolites-Phycosiphon ichnofabric characterizes intervals 3, 4 and 5. Fourteen ichnofabrics were differentiated in the core, mainly in view of lithological features, including ferruginous material, grain size, mottled background, ichnotaxa, and Bioturbation Index. A comparison between outcrop and core ichnofabrics through the upper 13.5m, corresponding to the uppermost Tortonian-lowermost Messinian interval, revealed certain similarities as well as some differences. A continuous and relatively slow siliciclastic deposition with punctual variations in the sedimentation rate can be interpreted that, associated with favorable paleoenvironmental parameters such as aerobic conditions and nutrient availability, evidence that a well-developed and diverse macroinvertebrate trace maker community existed at that time. Softgrounds are dominant, but occasionally loosegrounds and even firmgrounds could develop. The ichnofabric distribution shows long-range patterns in outcrop and core, and short-range patterns exclusively in core. Long-range patterns reflect the last phases of a transgressive system tract, with a “maximum flooding zone” at the end, and then a highstand normal regression. High-frequency, short-range, repetitive patterns in ichnofabrics from core, mainly between ichnofabrics 6/8 to 9 from lower to upper part of the pattern, can be linked to “local flooding surfaces”, subdividing the “maximum flooding zone” into parasequences. Our results reveals the usefulness of the integrative ichnofabric analysis, including outcrop and core materials, in sedimentary basin analysis, assessing paleoenvironmental conditions and improving sequence stratigraphy characterization.