Even though bacterivorous flagellates have been recognized as being able to structure the bacterial community, their behavioral basis for food selection is hardly known. We investigated the feeding behavior of the filter-feeding choanoflagellate Monosiga ovata and the raptorial-feeding kinetoplastid flagellate Rhynchomonas nasuta feeding on a bacterial community dominated by Pseudomonas putida and compared it to that of interception-feeding flagellates. M. ovata handles several food particles simultaneously. In contrast, R. nasuta handles only 1 particle at a time. The handling time for 1 prey particle is in the range of 3.7 s for R. nasuta but more than 300 s for M. ovata. The speed of food particles within the feeding current of M. ovata was only 9.3 +/- 5.7 mum s(-1) but due to the large surface of the collar the filtered water volume was 6.4 nl h-l and therefore comparable to that of interception-feeding flagellates of a similar size. Bacteria ingested by M. ovata were significantly smaller compared to the bacteria in the medium (p = 0.001). Size selection of food particles occurs during the processing of food items. This is in contrast to raptorial-feeding R. nasuta, which shows passive food size selection for bigger particles during the contact phase. Attachment of bacteria proved to be an efficient protection mechanism, defending them from being grazed by flagellates. There are significant species-specific differences in the processing of food particles which explain the coexistence of various bacterivorous nanoflagellates in the size range of 3 to 5 mum and indicate the existence of specific predation pressure on different bacteria.