Despite their large size and frequent occurrence in near-shore tropical habitats, little published information is available on the movements and behaviors of the giant manta ray, Manta birostris, and what factors influence visitation patterns. To examine the movements of manta rays in the Komodo Marine Park, Indonesia, an acoustic array was installed at up to seven sites in the park between 2000 and 2003. A total of 41 acoustic tags were deployed in three separate deployments in 2000, 2001 and 2002. Mantas were recorded in the park for up to 526 days with an average duration of 183 ± 136 days, when mantas made from 3 to 303 individual visits to different sites (median 58 visits). There was a clear preference for three sites that comprised over 90% of manta activity. The most popular site (German Flag) was off the southern tip of Komodo Island in an area with a high degree of bathymetric structure. Examination of the longest records suggests some site preference with 5 of 7 individuals spending greater than 90% of their time at the location where they were tagged. Using a general linear model it was possible to examine the effects of daytime, lunar phase, aggregation site, season and tidal phase on visitation patterns. The vast majority of visits were recorded during daylight hours at all sites. The strongest effects of both the lunar and tidal phase were apparent in the northern sites with the most visits occurring when tidal intensity was the greatest during full and new moons. The strongest seasonal pattern was observed in the south where no mantas were recorded during the first quarter in any year. This coincides with an increase in temperature and reduction of productivity in this region associated with monsoonal shifts. The long-term fidelity indicates that marine-protected areas centered around aggregation sites could help protect this species from overexploitation.