Past studies have argued that macroalgae serve as useful bioindicators that herald possible environmental changes to reef ecosystems because they are often opportunistic, having high growth rates and responding quickly to environmental changes, such as increased nutrient availability, grazing pressures, or storm activity. In this study, we test their usefulness as reef monitoring management indicators. We investigated the spatial and temporal variability of the relative abundance of macroalgae (RAM) at the genus level in the Mariana Archipelago between two surveys in 2003 and 2005. Islands vary drastically across the archipelago (carbonate vs volcanic, populated vs unpopulated, small vs large) and often experience considerable storm activity. We showed that the diversity of macroalgal genera was generally highest at the southern end of the archipelago, probably because of increased habitat heterogeneity around these geographically larger islands. At the northern end of the archipelago, only Pagan and Maug were large enough or contained enough environmental diversity to exhibit macroalgal diversity similar to that of the southern carbonate islands. Despite the ubiquitous nature of turf algae, crustose coralline red algae, and the green alga Halimeda (Bryopsidales) across the archipelago, multivariate analyses revealed RAM to differ among islands with northern, unpopulated, volcanic islands grouping together and differing from southern, populated, carbonate islands. Also, RAM showed significant variability at the local scale (among sites within an island) and over time. We hypothesize that this variability results principally from differing oceanographic conditions such as sea surface temperature, human impacts such as fishing and pollution, typhoons, and volcanic activity across the archipelago. These results provide a baseline for future monitoring studies in the Mariana Archipelago and suggest that rapid ecological assessments of macroalgae in the field at the genus level are a reliable indicator that can be used to monitor change over time.