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The deep scattering layers (DSL) in the central equatorial Pacific form an important prey resource in a relatively oligotrophic habitat. In March of 2006, we used a calibrated 38-kHz SIMRAD EK60 scientific sonar to assess the spatial distribution of the deep scattering layer relative to broad-scale oceanographic features and fine-scale physical and biological measurements. We conducted a single continuous transect from approximately 10°S to 20°N at 170°W while measuring acoustic backscatter, current velocity and direction, temperature, salinity, oxygen, and fluorescence with depth, coincident with marine mammal occurrence. These data were combined with remotely sensed sea surface height, chlorophyll, and sea surface temperature data to examine patterns in DSL distribution. To analyze DSL density with depth, acoustic backscatter was binned into surface (<200 m), mid (200–550 m) and deep (550–1000 m) layers. Backscatter was highly correlated with chlorophyll-a and low sea surface height anomalies and was greatest near the equator. We found high diel variability in DSL depth and scattering intensity between the mid and surface layers as well as a shallowing of the deep layer moving northward across the equator. Marine mammal sightings consisted primarily of odontocetes with their distribution coincident with higher acoustic densities of their forage base. Shifts in DSL distribution and scattering intensity are an important component towards understanding the behavior and distribution of highly migratory predator species.