The use of spatial analytical techniques for describing and classifying seafloor terrain has become increasingly widespread in recent years, facilitated by a combination of improved mapping technologies and computer power and the common use of Geographic Information Systems. Considering that the seafloor represents 71% of the surface of our planet, this is an important step towards understanding the Earth in its entirety. Bathymetric mapping systems, spanning a variety of sensors, have now developed to a point where the data they provide are able to capture seabed morphology at multiple scales, opening up the possibility of linking these data to oceanic, geological, and ecological processes. Applications of marine geomorphometry have now moved beyond the simple adoption of techniques developed for terrestrial studies. Whilst some former challenges have been largely resolved, we find new challenges constantly emerging from novel technology and applications. As increasing volumes of bathymetric data are acquired across the entire ocean floor at scales relevant to marine geosciences, resource assessment, and biodiversity evaluation, the scientific community needs to balance the influx of high-resolution data with robust quantitative processing and analysis techniques. This will allow marine geomorphometry to become more widely recognized as a sub-discipline of geomorphometry as well as to begin to tread its own path to meet the specific challenges that are associated with seabed mapping. This special issue brings together a collection of research articles that reflect the types of studies that are helping to chart the course for the future of marine geomorphometry.