Accurate fishery-independent methods for assessing the abundance of marine fish stocks are important tools for proper pelagic fisheries management. The review and improvement of standardized sampling methods used in fisheries-independent sampling, and the establishment of improved models of abundance and population dynamics utilizing novel statistical techniques for fisheries management will further improve our understanding of the way in which marine fish stocks vary spatially and temporally. One of the most important and longest running surveys of fisheries-independent data in the Southeastern United States is the spring ichthyoplankton survey conducted through the Southeast Area Mapping and Assessment Program (SEAMAP). These surveys of highly migratory pelagic fish larvae and eggs in the exclusive economic zone of the USA in the Gulf of Mexico have been conducted annually during spring spawning periods (March to June) since 1982 by the National Oceanic and Atmospheric Administration (NOAA) National Marine Fisheries Service (NMFS). A primary focus of this survey is collecting the data used in a larval abundance index of bluefin tuna (Thunnus thynnus) for "tuning" population estimates for the western Atlantic stock of this species using virtual population analysis (VPA). As with many other forms of fishery independent data, there is statistical overdispersion of larval fish and high variability in catch rates related to non-static environmental conditions. This variability in catch rates, along with zero-inflated estimates of abundance, i.e. characterized by high numbers of stations with low or zero catches, present problems in deriving accurate and reliable stock assessments for western Atlantic bluefin tuna. The research presented here was conducted in an effort to improve the decision support system used in managing bluefin tuna in the western Atlantic, by improving catch rates of their larvae during spring ichthyoplankton cruises. A major focus of which was to overcome challenges related to reducing the variance of the larval index of abundance. The research presented here, explored the influence of sampling design and oceanographic conditions on an assemblage of commercially important taxa within the Gulf of Mexico. Such studies are necessary to evaluate differences in habitat utilization within a specific complex or among assemblages of closely related taxa. The spatial and temporal patterns of larval bluefin tuna (Thunnus thynnus) were analyzed in relation to mesoscale patterns of circulation, types of sampling gear used during fishery independent surveys, and in the context of common oceanographic variables associated with the spawning habitat of this iconic pelagic predator. Collaterally the relationship between the above factors on spatial and temporal patterns of the larvae of seven congeneric species of marine fish, whose larvae commonly occur with bluefin tuna, during the spring spawning season in the Gulf of Mexico (Auxis spp., Euthynnus alleteratus Corphaena spp., Katsuwonus pelamis, other Thunnus spp.: Thunnus albacares and Thunnus atlanticus, Istiophoridae, and Xiphias gladius) was investigated. The historical distribution of abundance in these eight taxa of larval epipelagic fish were analyzed in the context of mesoscale and large scale circulation features in the Gulf of Mexico between 1994 and 2008. Characterization of these features was conducted using concurrent, synoptic satellite altimeter, sea surface temperature (SST), and ocean color (OC) observations. Larval abundance among mesocale features was examined for the eight pelagic fish taxa using permutational multivariate analysis of variance (PERMANOVA). All but one taxon, T. thynnus, showed differences in occurrence across features. Additionally only two taxa (X. gladius and Istiophoridae) did not show highest abundances in "Common Waters" of the Gulf of Mexico. The abundance of the eight taxa, when examined in aggregate or as an assemblage, differed significantly between circulation features. However, distributions of individual taxa among circulation features differed for only the other Thunnus spp. taxa, which incorporates Thunnus albacares and atlanticus. The results from this study indicated that for most of the individual taxa studied, and Thunnus thynnus in particular the distribution of spawning habitat in the Gulf of Mexico is not associated with specific patterns in circulation. To analyze the impact of sampling gear on larval epipelagic abundance, the collection methods of the eight taxa during spring surveys, including a new net sampling methodology tested in surveys between 2009 and 2011, were compared. This new sampling methodology consisted of a 1x2 m frame fitted with a 0.505 mm mesh net, towed in a yo-yo fashion between the surface and 10m depth, referred to as the S-10 net. Sampling effectiveness between gears was compared by examining the abundance and length of the eight taxa of larval fish. A PERMANOVA of net type and time of sampling (day/night) on abundance and mean body length (BL) indicated that net type was a significant factor in assessing abundance and BL for all taxa. Highest mean assemblage and individual taxa abundance for seven of the eight taxa were in S-10 samples. Depth discrete sampling of the upper 50 m indicated that highest abundances for all scombrid taxa were found in the upper 30 m and provided justification for the improved sampling efficiency of the S-10 net. These results indicate that distributions of these epipelagic fish are not truly neustonic and that sampling effectiveness for them strongly depends on depth range fished by the net. Finally, the results of two research cruises using the new sampling methodology (S-10 net) during the spring of 2010 and 2011 were investigated to explore larval fish assemblages. Canonical analysis of principal coordinates (CAP) was used to evaluate the horizontal distribution of eight taxa of epipelagic larval fish and to relate these distributions to a total of eight variables observed through in-situ and remotely obtained data. Larval assemblages were established for the CAP via unweighted pair group method with arithmetic mean (UPGMA) hierarchical clustering utilizing similarity profile analysis (SIMPROF) tests for stopping rules. Further refinement to five common assemblage groups was obtained using indicator species values (INDVALS) and percent composition of taxa abundance within groups. Total model accuracy was 54%, with highest classification success for the assemblage group characterized by T. thynnus and the other Thunnus spp. (64%), and lowest classification success for negative stations (22%). Changes in the assemblage of these larval fish were partially explained by the seasonal progression in day-length, and related changes in sea surface temperature. Depth, chlorophyll a concentration, salinity, and optical clarity were also important. Five assemblages of larval fish were identified, characterized by differences in the relative abundance of the five taxa of scombrids, and the Coryphaena spp. taxa, and indicated a high degree of shared spawning habitat. The differences in habitat utilization by these taxa is highly influenced by seasonal changes in sea surface temperature, and large scale differences in depth and water masses in the Gulf of Mexico. This results in a gradual shift from groups with smaller and more abundant coastally influenced taxa with protracted spawning seasons to the larger sub-tropical, more pelagic species across a large expanse of shared spawning habitat. This dissertation research provides a context to the historical assessment of abundance, evidence for the association of specific taxa with particular oceanographic conditions, and improved assessment capabilities for epipelagic larval fish. As this research shows the spawning habitat of these taxa in the Gulf of Mexico are largely shared, and the influence of environmental variables only partly addressed the spatial and temporal variance attributed to larval abundance in the Gulf of Mexico. The improved methods used in this study will be useful to researchers studying the factors impacting larval recruitment and survival of highly migratory species, and comprehensive ecosystem based resource management. The results will improve fisheries-independent sampling and management for highly migratory species, and provides new methods for evaluating larval fish assemblages within the framework of oceanographic conditions for large marine ecosystems.