Two oysters, the native flat oyster, Ostrea edulis, and the non-indigenous Pacific oyster, Crassostrea gigas, have partially overlapping distributions in European waters. Relatively little is known about particle selection by O. edulis, and the goal of the present study was to establish baselines for particle selection by both oyster species under controlled conditions in the laboratory. The study was carried out with adult oysters of similar shell size collected in the Limfjord estuary, Denmark (56°47′N, 08°51′E), in November 2011. The feeding traits of both species [clearance rate (CR), retention efficiency (RE) and lower threshold for clearance (LTC)] were compared using five algal species with different cell sizes (5−32 µm ESD) (Isochrysis galbana, Rhodomonas salina, Thalassiosira weissflogii, Prorocentrum micans and Akashiwo sanguinea). Oysters were acclimated to an experimental temperature of 22 °C and a salinity of 25. The CR of O. edulis was one to three times lower than that of C. gigas for the three smaller algal species (5−15 µm) but not different for the two larger algae. Algae in the size range 7−32 µm were retained with 100% RE by both oysters, but the smallest alga was retained with reduced RE (~35%). There were no differences in LTC between the two oysters. A closer examination of the relationship between LTC and different measures of the algae present (cell size, cell volume, chl a, C and N) suggests that the LTC, and also the CR, may depend in part on the internal energy status of the oysters.