Reef structural complexity provides important refuge habitat for a range of marine organisms, and is a useful indicator of the health and resilience of reefs as a whole. Marine scientists have recently begun to use ‘Structure from Motion’ (SfM) photogrammetry in order to accurately and repeatably capture the 3D structure of physical objects underwater, including reefs. There has however been limited research on the comparability of this new method with existing analogue methods already used widely for measuring and monitoring 3D structure, such as ‘tape and chain rugosity index (RI)’ and graded visual assessments. Our ﬁndings show thatanalogueandSfMRIcanbereliablyconvertedoverastandard10-mreefsection (SfM RI = 1.348 chain RI—0.359, r2 = 0.82; and Chain RI = 0.606 SfM RI + 0.465) for RI values up to 2.0, however, SfM RI values above this number become increasingly divergent from traditional tape and chain measurements. Additionally we found SfM RI correlates well with visual assessment grades of coral reef over a 10 10 m area (SfM RI = 0.1461 visual grade + 1.117; r2 = 0.83). The SfM method is shown to be affordable and non-destructive whilst also allowing the data collected to be archival, less biased by the observer, and broader in its scope of applications than standard methods. This work allows researchers to easily transition from analogue to digital structural assessment techniques, facilitating continued long-term monitoring, whilst also improving the quality and additional research value of the data collected.