A controlled-source audio-frequency magnetotelluric (CSAMT) survey was conducted over Toya caldera, Hokkaido, Japan, to investigate its subsurface structure. The caldera is 10⊖11 km in diameter and contains a freshwater lake, Lake Toya, that occupies the entire caldera floor. A post-caldera dacitic dome complex, the Nakajima Islands, is present within Lake Toya. The CSAMT survey was carried out along a 16-km-long line that crosses Toya caldera in a NE⊖ SW direction, passing over the Nakajima Islands. The 17 receiver stations (7 stations located outside of Lake Toya, 5 stations within Lake Toya, and 5 stations on the Nakajima Islands) were distributed along the survey line. Unique on-boat measurements were performed at the stations on Lake Toya. Two-dimensional inversion of the CSAMT data revealed the resistivity structure for the upper 1500 m beneath the caldera. The resistivity structure indicates the existences of high-resistivity (> 100 Ω×m) and low-resistivity (< 30 Ω×m) domains at the northeastern and southwestern sides of Lake Toya, respectively, a medium-resistivity (30⊖50 Ω×m) domain beneath Lake Toya, a high-resistivity (> 100 Ω×m) layer at the Nakajima Islands, and a lowresistivity (< 10 Ω×m) domain beneath the Nakajima Islands. This resistivity structure, combined with geological and bathymetric data, suggests that the subsurface structure of Toya caldera comprises altered Tertiary to Quaternary volcanic/sedimentary rocks outside of the caldera, and a homogeneous caldera-fill deposit beneath the caldera floor. A 9-km-diameter ring fault may occur along the caldera rim. There is a conspicuous hydrothermal alteration zone beneath the Nakajima Islands that may have formed in response to heating of the caldera-fill deposit by the underlying magma during the volcanic activity that formed the Nakajima Islands.