Paleontological and sedimentological analyses were carried out in sediment core from southeastern Mediterranean Sea, offshore Egypt to reconstruct the past environmental changes in trophic state and temperature during Holocene. To achieve our goals, grain size, total organic carbon, planktic and benthic foraminifera, dinoflagellate cysts have been investigated. Few micropalaentological studies have been done in the studied area and none of them used the combined proxies of benthic foraminifera and dinoflagellate cyst. Theses combined proxies reflects more comprehensive paleoenvironmental view. Biotic and abiotic data have been analysed with multivariate technique including Redundancy Analysis (RDA). Diversity indices such as: Fisher alpha index (α) and Shannon index (H) have been applied. The foraminiferal study yields 9 planktic species and 10 benthic species. Foraminiferal assemblages have low species diversity indices especially at sapropel layer S1. Mediterranean sapropels are layers with elevated organic carbon concentrations that contrast with surrounding organic poor sediments. Sapropels occur periodically in sedimentary sequences of the last millions years, which have been the subject of extensive previous study. Redundancy Analysis (RDA) yields two groups of foraminiferal assemblages depending on the changes of total organic carbon and clay content. The dinocysts study yields 15 species, the majority of cyst types belonging to the order Gonyaulacales. The association of dinoflagellate cyst shows two depositional phases in the sediment. The sapropel layer S1, with anoxic condition and warmer temperature, is recorded at depth 28−46 cm where heterotrophic taxa dominate and the post-sapropel layer is recorded at depth 0-28 cm; where autotrophic taxa dominate.