Deep-sea fishes on seamounts have recently been shown to have strong changes in assemblage patterns with depth. However, horizontal variability patterns within a single seamount and among seamounts remain drastically understudied. The Papahānaumokuākea Marine National Monument (PMNM) is part of an extensive seamount chain that is relatively unimpacted by human activity as well as highly variable in physiographic and oceanographic characteristics. Three PMNM seamounts, Necker Island, French Frigate Shoals (FFS), and Pioneer Bank, were explored using Autonomous Underwater Vehicle surveys to document the deep-sea fish assemblages and their horizontal patterns of distribution at three different depths. Quantitative comparisons were made among the sides of the seamount and among the three seamounts while controlling for depth. The Gadiformes were the most abundant order with the highest number of individuals at 300 and 450 m on Pioneer and FFS. At 600 m the Myctophiformes showed the highest number of individuals overall and were the most abundant on FFS. Significant differences in abundance by seamount, side, and their interaction were observed at 300 and 600 m. Significant differences in some diversity metrics occurred in one, both, or the interaction of the factors of seamount and side at each depth. At all depths, the structure of the fish assemblage showed significant variation among seamounts and sides, which was explained mostly by the interaction term. After accounting for the variability explained by the confounding factor of time of day, the most common environmental factors related to assemblage structure for at least two depths were the east-west component of currents (u), latitude, chlorophyll a (chl a), and particulate organic carbon (POC). At 300 m, oxygen and salinity were also important, at 450 m mean direction of the substrate was an additional factor that was correlated with assemblage structure. At 600 m the factor that explained the most variation in community structure was percent rugosity. The results obtained in this study show significant horizontal variability in seamount fish assemblages within a given depth range; this variability should be taken into consideration in the management and conservation of the Monument and other seamounts.