Hydrogenetic ferromanganese crusts (hereafter referred to as “crusts”) on Pacific seamounts are formed by the precipitation of iron–manganese oxides from seawater on volcanic and biogenic substrate rocks. As crusts grow continuously and have very slow growth rates of between 1 and 10 mm/m.y., they can potentially be used as records of the Neogene paleoceanographic and paleoclimatic conditions. Crusts can be considered as compressed sediment cores containing biogenic, volcanogenic, and terrestrial particles that include eolian dusts and the partly weathered products of substrate acquired during its growth. In this study, selective leaching experiments were conducted on a sample of ferromanganese crust, which had been obtained from the Federated States of Micronesia at a water depth of 2262 m. Chemical leaching experiments were conducted using oxalic acid buffered with ammonium oxalate on the crushed crust samples, which is an optimization of previously proposed sequential leaching procedures. The applied method was found to be effective in separating the major mineral phases of crusts from associated metallic components, thereby providing concentration of the residual fraction for use in analysis following the leaching experiment. Using this method, polygenetic particles were extracted from the crust and identified using optical and electron microscopes. They were found to be of various origins and included volcanogenic, biogenic, terrestrial, and extraterrestrial material. In addition, well-sorted prism-shaped chained magnetic particles were observed in residual fractions. Rock magnetic experiments support the idea that the magnetic particles are magnetites and originated from fossil magnetotactic bacteria. The fossil magnetotactic bacteria might have been living on the crust at the time of crust formation. Alternatively, fossil magnetotactic bacteria could have been transported by deep sea currents from the sediment where magnetotactic bacteria originated.