Understanding the effects of scale is essential to the understanding of natural ecosystems, particularly in marine environments where sampling is more limited and sporadic than in terrestrial environments. Despite its recognized importance, scale is rarely considered in benthic habitat mapping studies. Lack of explicit statement of scale in the literature is an impediment to better characterization of seafloor pattern and process. This review paper highlights the importance of incorporating ecological scaling and geographical theories in benthic habitat mapping. It reviews notions of ecological scale and benthic habitat mapping, in addition to the way spatial scale influences patterns and processes in benthic habitats. We address how scale is represented in geographic data, how it influences their analysis, and consequently how it influences our understanding of seafloor ecosystems. We conclude that quantification of ecological processes at multiple scales using spatial statistics is needed to gain a better characterization of species-habitat relationships. We offer recommendations on more effective practices in benthic habitat mapping, including sampling that covers multiple spatial scales and that includes as many environmental variables as possible, adopting continuum-based habitat characterization approaches, using statistical analyses that consider the spatial nature of data, and explicit statement of the scale at which the research was conducted. We recommend a set of improved standards for defining benthic habitat. With these standards benthic habitats can be defined as ‘areas of seabed that are (geo)statistically significantly different from their surroundings in terms of physical, chemical and biological characteristics, when observed at particular spatial and temporal scales’.