We have studied benthic foraminiferal assemblages in a marine sediment section (Pefka E section) from the Lindos Bay Formation deposited during the early Pleistocene to provide new insights into the paleo-ecologic and neotectonic evolution of the SE part of the island of Rhodes (NE Mediterranean Sea). Relatively high amounts of eutrophic/low oxygen tolerant species and a comparatively high foraminiferal diversity indicate generally mesotrophic conditions at the sea floor and the presence of well-oxygenated bottom waters. These conditions are attributed to generally elevated surface water productivity and related organic matter fluxes during the early Pleistocene, which is in contrast to the modern oligotrophic conditions in this region. The abundance of individual species shows orbital-driven variability in the obliquity (41 kyr) and precessional (∼23 kyr) bands. Obliquity-driven changes in food availability are indicated by increased percentages of Cassidulina carinata s.l. during marine isotope stages (MIS) 44 and 42, reflecting enhanced food fluxes under glacial conditions. Precession-driven changes are observed for Ca. carinata s.l., Cibicidoides pseudoungerianus s.l., Cibicidoides mundulus and Gyroidinoides altiformis. These changes likely reflect prolonged near-coastal phytoplankton blooms triggered by local fresh-water runoff at times of Northern-Hemisphere insolation maxima, coeval to the formation of sapropels in the adjacent deep-sea basins. The application of a benthic foraminiferal transfer function allowed for the identification of a number of short-term subsidence-uplift cycles, superimposed by overall long-term subsidence of the SE coast of Rhodes. Estimated average uplift and subsidence rates vary between ∼4.2 and ∼10.3 mm/yr. These rates of tectonic motions are distinctly higher compared to most other estimates from Rhodes and suggest a complex neotectonic history of the island during the early Pleistocene, involving both large-scale and local motions associated with alternating compressional and extensional regimes.