As anuran biodiversity quickly declines, it is important to understand local patterns of anuran occurrence. However, the limitations of traditional sampling methods make anuran biodiversity surveys inadequate. Tropical environments are rich in anuran species, which makes biodiversity measurements more difficult. Therefore, it is important to develop a rapid, inexpensive and nondestructive method to measure anuran biodiversity in tropical environments. We used eDNA metabarcoding to measure anuran diversity at 288 sites in 18 regions of Hainan Island. We also used traditional methods and compared the results with those obtained through the eDNA metabarcoding methods. We detected 9 anuran species by traditional sampling methods. We produced 626 million reads by eDNA metabarcoding and assigned them to 15 anuran species. Therefore, eDNA metabarcoding can be used for rapid and large-scale anuran biodiversity surveys.

The species–area relationship is important for understanding species diversity patterns at spatial scales, but few studies have examined the relationship using environmental DNA (eDNA) techniques. We investigated amphibian diversity on 21 islands of the Zhoushan Archipelago and nearby mainland areas in China using the combination of eDNA metabarcoding and the traditional line transect method (TLTM) and identified the species–area relationship for amphibians on the islands. The mean detection probability of eDNA is 0.54, while the mean detection probability of TLTM is 0.24. The eDNA metabarcoding detected eight amphibian species on the islands and nine species in the mainland areas, compared with seven species on the islands and nine species in the mainland areas that were identified by TLTM. Amphibian richness on the islands increased with island area and habitat diversity. The species–area relationship for amphibians in the archipelago was formulated as the power function (S = 0.47A^0.21) or exponential function (S = 2.59 + 2.41 (logA)). Our results suggested that eDNA metabarcoding is more sensitive for the detection of amphibian species. The combined use of eDNA metabarcoding and the traditional line transect method may optimize the survey results for amphibians.