Biodiversity has faced a steep decline during the Anthropocene and as human influence on ecosystems through the direct impacts of development and indirect impact of climate change continue to increase the threat to global biodiversity is higher than ever. Coastal marine ecosystems are particularly susceptible to human activities due to their proximity to human settlements and ease of access. In order to protect coastal oceans, it is important to accurately catalog the biodiversity of these recreationally and commercially valuable ecosystems, but marine systems differ in the mechanisms that drive population structure and incipient speciation common to terrestrial systems. Large population size, a lack of physical barriers, and high dispersal potential make it a challenge to identify reproductively isolated populations in marine environments. Molecular techniques have provided solutions to some of these challenges as they are capable of determining where populations fall on the continuum between panmixia and speciation and allow investigators to identify previously undescribed biodiversity (interspecific and intraspecific genetic variation) in marine ecosystems. In this dissertation I use genome-wide sequencing techniques to search for patterns of cryptic speciation and explore the population dynamics of fishes from the family Clinidae in two dynamic coastal ecosystems, Southern Africa and Western North America.