Ostracodes are the only commonly preserved deep-ocean metazoans and thereby provide an important perspective on bottom-water conditions during the Paleocene-Eocene Thermal Maximum (PETM). At Southern Ocean ODP Sites 690 (Maud Rise, Atlantic Sector) and 738 (Kerguelen Plateau, Indian Sector), ostracode abundance abruptly decreases at the onset of the carbon isotope excursion (CIE), and then increases within the PETM, with approximately 2/3 to total recovery following the PETM. The Site 690 fauna is taxonomically richer overall than that of Site 738, and shows less taxonomic loss within the CIE. Site 738 richness recovers following the CIE, while Site 690 richness remains low, perhaps reflecting lingering deleterious conditions. Faunal analyses demonstrate that Site 690 consists of three distinct faunas bounded by the CIE and subsequent recovery to relatively stable oxygen and carbon isotope values. A similar, but less robust, faunal pattern is present at Site 738, perhaps due to sampling of lower-resolution and smaller-volume. The rapid recovery in ostracode abundance following the CIE does not support prolonged bottom-water dysoxia through the PETM. Furthermore, the proportion of dysoxia-tolerant filter-feeding taxa does not increase coincident with or immediately following the CIE, as would be expected under dysoxic conditions based on physiological principles and other dysoxic environments (e.g., Cretaceous OAEs, modern OMZs). Instead, the percent of filter-feeder taxa increases as abundance recovers, perhaps in response to increasing surface export production in the later PETM. The stratigraphic restriction of specific taxa to specific CIE intervals provides a paleoecological registry that may be tested at other PETM sites and throughout the early Paleogene. This comparative approach can provide feed-back on both environment and ecology, and thereby allow a more complete reconstruction of this brief, but globally significant, warming event.