The formation of the Baja California peninsula separated the distributions of 19 marine fishes into disjunct Pacific and Sea of Cortez populations. Similarly, their Pacific distributions cross phylogeographic points that diminish the genetic connectivity of their populations. This resulted in multiple species experiencing a gradient of gene flow and an extraordinary framework to study mechanisms of divergence and signals of selection under different scenarios of isolation. Genetic isolation in these species has previously been studied using only a handful of markers. In this dissertation, Restriction Site-Associated DNA (RADseq) is used to genotype thousands of genome-wide makers to study the evolutionary history, characterized genomic patterns of divergence among populations, and search for signals of drift and selection, in four of these species: the sargo, Anisotremus davidsonii (ADA); the longjaw mudsucker, Gillichthys mirabilis (GMI), the California sheephead, Semicossyphus pulcher (SPU); and the zebraperch, Kyphosus azureus (KAZ). While, no evidence of isolation was found for SPU, estimated dates the disjunction of ADA, GMI, and KAZ, were 60, 284, and 23 thousand years, respectively. A dispersal episode where species migrated northwards and then became isolated by the warming of the seawater temperate in the south of the Baja California peninsula at the end of the last glaciation period, and a vicariant isolation resulting from the closure of a mid-peninsular seaway, are the plausible historical events that produced the current distributions of these species. Lower than expected levels of genomic gene flow (significant p-values) were seen across Point Conception in GMI (FST=0.15), Punta Eugenia in ADA (FST=0.02), and across the peninsula in KAZ, GMI and ADA (FST=0.03, 0.11, and 0.23, respectively). Furthermore, when comparing disjunct populations, 19 to 46 % of outlier loci matched coding genes in all species and analyses identified 15 genomic regions, potentially involved in processing environmental information, metabolism, immune response, and possibly reproduction, diverging in more than one of these species. Results are interpreted as supporting (1) the idea that ADA and GMI disjunct populations are in the initial phases of allopatric speciation and (2) the presence of convergent selection in these species.