|The carangiform fishes, which include approximately 1,100 species in 29–34 families, were initially recovered as a clade in DNA-based studies. Subsequent to its initial recovery, many molecular phylogenies have been published assessing carangiform relationships, but these studies present a conflicting array of hypotheses on the intrarelationships of this clade. In addition to this diversity of hypotheses, no studies have explicitly diagnosed the clade or its major subgroups from a morphological perspective or conducted a simultaneous analysis to put forth synapomorphies for relationships across the Carangiformes using a combination of molecular and morphological data. In the first chapter of this dissertation, we performed combined analyses of new and previously identified discrete morphological characters and new and previously published genome-scale data to characterize the evolutionary history and anatomical variation within this clade of fishes. Our combined analysis of these data resulted in a monophyletic Carangiformes, with a series of subclades nested within. We put forth a series of subordinal names based on the recovered branching pattern, morphological character evidence, and relative stability in large-scale studies. In the second and third chapters of this dissertation, we take a deep-dive into the evolutionary relationships among two families of carangiform fishes with distinct morphologies and noticeable habitat shifts that are not well understood from an evolutionary standpoint. The first family is the Polynemidae or threadfins. This group of roughly 40 species are easily differentiated from other fishes due to their numerous, elongated, and thread-like pectoral-fin rays extending from the pectoral region. All species of threadfins possess these free pectoral-fin rays, but both the number of free filaments and length of the free filaments varies widely across the family. The majority of systematic works to include the Polynemidae have focused on the interrelationships of the family, with three previous theses focusing on the intrarelationships of the threadfins. Curiously, the most species-rich genus of threadfin, Polydactylus, has been recovered polyphyletic in all three previous theses. In order to answer questions about threadfin taxonomy and character evolution, we take an integrative approach, using combined analyses of hard- and soft-tissue discrete morphological characters with new and previously published genetic data to construct a combined phylogeny of the threadfins. Our analyses highlight the non-monophyly of Polydactylus and we describe seven new genera to represent these polyphyletic lineages. Our analyses also highlight a wealth of convergently evolving characters within the threadfins. We discuss not only characters that optimize in support of the relationships we recover, but also patterns of morphological convergence within the Polynemidae. The second family we investigate are the archerfishes in the Toxotidae, which are well known for their ability to project a jet of water from the mouth at terrestrial prey items. These streams of water are intended to strike their prey item and cause it to fall into the water for capture and consumption. However, we do not know if all archerfishes possess the oral structures thought to form and project the jet of water from the mouth, if anatomical variation is present within these oral structures, or how this mechanism has evolved. Further, there is little information on the evolution of Toxotidae as a whole, with all previous systematic works focusing on the interrelationships of the family. We first investigate the limits of archerfish species using genetic data. Our analysis highlights that the current taxonomy of archerfishes does not conform to the relationships we recover and we synonymize two currently-described species of archerfishes and elevate two taxonomic synonyms based on the branching pattern we recover. We then take an integrative approach, using a combined analysis of hard- and soft-tissue discrete morphological characters with genetic data, to construct a phylogeny of Toxotidae. The resulting phylogenetic hypothesis allows us to discuss the variation present within the archerfish oral structures and the evolution of the mechanism in light of other members of Toxotoidei. Although two of the three previous chapters in this dissertation put forth hypotheses of relationships for two carangiform families that have noticeable patterns of habitat transitions, we still did not have a broad view of the habitat transitions occurring within the carangiform radiation. The Carangiformes survive within a remarkable variety of habitats, including coastal brackish environments, deep demersal continental slopes, and freshwater lakes and rivers. As percomorph clades rarely inhabit such a range of environments, the Carangiformes represent an unusual amount of habitat variation amongst the crown group of fishes. To investigate habitat transitions across the carangiform fishes, we generate a synthetic supertree of the clade. Our analyses and optimizations of habitat salinity highlight the repeated and taxonomically limited invasions of brackish- and freshwaters across the carangiform lineage, with four families returning to a habitat of higher salinity from a freshwater ancestor. We also find that, although the euryhaline condition has evolved numerous times across the evolution of the Carangiformes, only one family is characterized by the ability to traverse habitats of various salinity levels.