This dataset was collected at six sites on four reefs across Taiwan’s tropical and subtropical regions between April and July 2019. The two reefs in the tropical region were Tiaoshi in the south and Kihaw in the southeast of Taiwan Island. The other two reefs in the subtropical region were Chinwan Inner Bay in the Penghu Archipelago and Yehliu in northern Taiwan. The six sites included two depths in Yehliu (3 m and 6 m) and Tiaoshi (5 m and 10 m), but only one depth each in Kihaw (3 m) and Chinwan Inner Bay (3 m) because these two had no suitable reef communities located deeper than 5 m. 

Three consecutive transects were placed, according to reef contouring, continuously a few meters apart along depth contours parallel to the shoreline at each site. Alternatively, three transects were deployed in parallel for short reefs. The standard transect length used in this dataset was 15 m. However, one transect at the shallow depth of Tiaoshi was 14 m long because of operator error. A total of 18 transects at six sites were surveyed.

We applied the ten categories of Reef Check’s Tropical Program protocol (Hodgson et al., 2006) to classify benthos and substrates, including hard coral (HC), soft coral (SC), recently killed coral (RKC), nutrient indicator algae (NIA), sponge (SP), rock (RC), rubble (RB), sand (SD), silt/clay (SI), and other substrates (OT). In addition, hard corals, including the scleractinians, Heliopora and Millepora, were identified to species level, and rock was divided into rock (RC), turf algae (TF), and crustose coralline algae (CCA).

The quantification of each benthic category on each transect was first calculated using the Line Intercept Transect (LIT) method. Briefly, the substrate type at each sampling point with one cm interval was assigned to one of the categories above. The percentage cover of each category on each transect was calculated by dividing the cumulative points of the category by the total points of the transect (1400 or 1500 points for 14 or 15 m transects, respectively). 

Detailed information is listed in the "README_Kuo_et_al_2022_BenthicCommunityComposition_raw.txt" file.