Three-dimensional magnetotelluric (MT) inversion is an emerging technique for offshore hydrocarbon exploration. We have developed a new approach to the 3D inversion of MT data, based on the integral equation method. The Tikhonov regularization and physical constraint have been used to obtain a stable and reasonable solution of the inverse problem. The method is implemented in a fully parallel computer code. We have applied the developed method and software for the inversion of marine MT data collected by the Scripps Institution of Oceanography (SIO) in the Gemini prospect, Gulf of Mexico. The inversion domain was discretized into 1.6 million cells. It took nine hours to complete 51 iterations on the 832-processor cluster with a final misfit between the observed and predicted data of 6.2%. The inversion results reveal a resistive salt structure, which is confirmed by a comparison with the seismic data. These inversion results demonstrate that resistive geoelectrical structures like salt domes can be mapped with reasonable accuracy using the 3D inversion of marine MT data.