Thraustochytrids, osmoheterotrophic protists which are decomposers in the marine ecosystem, are emerging as promising sources of valuable lipids such as docosahexaenoic acid and squalene. To decompose organic macromolecules in their environment, they are thought to secrete degradation enzymes. However, at present, the secretome analysis of thraustochytrids is still insufficiently studied. In this study, we attempted to identify extracellular proteins secreted by Aurantiochytrium sp. 18W-13a, a thraustochytrid strain that has high squalene content. Supernatants of cultures grown under standard growth media were concentrated and the obtained proteins were fractionated and identified using mass spectrometry. Two proteins, SP1 and SP2, were identified and found to be constitutively expressed. SP2 contains von Willebrand factor A and PAN/APPLE domains, which are involved in protein adhesion. Extracellular proteins from this strain may have roles related to protein or ligand interactions and may be necessary for the cell’s survival.