We conducted a multi-proxy study on suspended particulate matter (SPM) sampled in depth profiles along two transects in the oligotrophic central equatorial Indian Ocean. The aim of the study is to better understand the sources and fate of organic matter carried by SPM in this rarely studied oligotrophic ocean. In this region organic matter may be an important food source as primary productivity and sinking fluxes are very small with little seasonal variation. To characterize SPM source and degradation state of organic matter, we combined bulk stable isotope and amino acid analyses with compound specific stable isotope analyses (CSIA) of carbon and nitrogen of amino acids. Based on nitrogen CSIA we found that there was no change in trophic position but indications of increasing bacterial heterotrophic resynthesis from the epi- to mesopelagic ocean. Changes of carbon CSIA revealed a mixed source planktonic and bacterial organic matter. Furthermore, we observed significant changes of carbon CSIA between epi- and mesopelagic samples but no further significant changes with depth within the mesopelagic zone. Our findings are consistent with previous SPM studies and support the idea that there is little qualitative or quantitative change in organic matter on SPM with increasing water depths below the epipelagic zone. SPM may thus be a source of relatively fresh organic matter at depth.