The Earth's oceans are inherently 3-D in nature. Many physical, environmental, and biotic processes vary widely across depths. In recent years, human activities, such as oil drilling, mining, and fishing are rapidly expanding into deeper frontier ocean areas, where much of the biodiversity remains unknown. Most current conservation actions, management decisions and policies of both the pelagic and benthic domains do not explicitly incorporate the 3-D nature of the oceans and are still based on a two-dimensional approach. Here, we review current advances in marine research and conservation, aiming to advance towards incorporating the third dimension in marine systematic conservation planning. We highlight the importance and potential of vertical conservation planning and zoning from the sea surface to the seafloor. We propose that undertaking marine conservation, management and environmental decisions in 3-D has the potential to revolutionize marine conservation research, practice and legislation.