We present a comprehensive description of the analysis of marine magnetic vector anomalies. The marine magnetic vector field can be measured with a shipboard three‐component magnetometer (STCM). The STCM has the advantage of measuring three components, but it suffers from several types of noise sources because the principles of its measurement are more complex than that of a proton‐precession magnetometer. We have estimated the quality of STCM data, constructed an optimal filter, and evaluated the reliability of the filtered data. Then, we have organized an analytical procedure composed of four steps: (1) the discrimination between two‐ and three‐ dimensional magnetic sources; (2) the determination of magnetic boundaries; (3) the calculation of the boundary strikes; and (4) the estimation of the boundary magnetization contrasts. We show examples of these procedures using the data near the East Pacific Rise 28°S–31°S collected during leg 5 of the GLORIA expedition. All the results of the above processing are merged in order to illustrate the distinct pattern of the seafloor magnetization in the su