The occurrence of early diagenetic Ca-rhodochrosite [(Mn,Ca)CO3] is reported in association with ‘griotte’-type nodular limestones from basinal settings in the geological record; however, without the comparison of analogous modern examples, the controls on precipitation remain speculative. Here the findings of four layers of primary Ca-rich rhodochrosite recovered from a modern deep-sea setting in the Eastern Equatorial Pacific, from bioturbated sediments 300 m below sea floor, are reported (Ocean Drilling Program, Leg 201, Site 1226). The mineralogy is similar to cements in burrows recovered during Deep Sea Drilling Project Leg 68 at Eastern Equatorial Pacific Site 503 and from Ca-rhodochrosite laminae in sediments of the central Baltic Sea. Petrographic relationships and constant oxygen isotopic compositions in the Ca-rhodochrosite around 5‰ at all depths indicate a shallow burial depth of formation. The onset of 1‰ heavier oxygen isotope composition of Ca-rhodochrosite at Site 503, about 30 m below the Pliocene/Pleistocene boundary, further suggests that precipitation occurs in the range of 30 m below sea floor. The approximate depth of formation allowed an approximate empirical fractionation factor for marine Ca-rhodochrosite to be constrained that strongly differs from previously published theoretical values. Based on the approximate precipitation depth, authigenic Ca-rhodochrosite forms within the SO42−-reduction zone. Moderately negative δ13C values (around −3‰) and total organic carbon lower than 2 wt% indicate a relatively low contribution of CO32− from organic C mineralization within the expanded redox zonation in the Eastern Equatorial Pacific. It is suggested that the alkalinity is increased by a rise in pH at focused sites of Mn-reduction coupled with S2− oxidation. High concentrations of Mn-oxide can accumulate in layers or burrows because of Mn-cycling in suboxic sediments as suggested for the Baltic Sea Ca-rhodochrosites. This study demonstrates how early diagenetic precipitates document biogeochemical processes from past diagenetic systems.