As a consequence of climate change, thermal stratification in lakes strengthens and increases the tendency towards hypolimnetic hypoxia or even anoxia. In the boreal zone, numerous lakes already undergo seasonal hypolimnetic anoxia, but its consequences for the microbial food web (MFW) are still largely unknown. However, the abundance as well as vertical distribution of predators, especially ciliates, in the MFW is generally assumed to be controlled by food and oxygen availability. To determine whether oxygen regulates the MFW, we studied the autotrophic picoplankton (APP), larger phytoplankton, bacteria, nanoflagellates (NFs) and ciliates present throughout the growing season in a small, humic and seasonally strongly stratified lake (ValkeaKotinen) with an anoxic hypolimnion. The prey numbers in Lake Valkea-Kotinen were low, whereas the predators were numerous. The abundance of NFs, which was coupled with that of bacteria, was especially high. However, our results indicated no clear response to oxygen conditions, although the abundances of the predators were generally higher in the oxic than in the anoxic water layers. The only ciliate feeding group that showed a clear response was the omnivores, which thrived in the hypoxic hypolimnion in early summer. The APP and bacterial abundances were in general high in the upper hypolimnion near the thermocline, which in Lake Valkea-Kotinen is prone to convective mixing. This diurnal disturbance nurtures the autotrophic and heterotrophic community around the thermocline and may also explain the rather high predator abundance in the MFW of Lake Valkea-Kotinen.