The aim of this work was to study freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. We followed their absolute abundance in oligotrophic Lake Constance (Germany) with quantitative polymerase chain reaction (qPCR) over a time frame of two consecutive years from November 2017 until November 2019. During this time we took water samples monthly (2017/2018) or as required (2019) at a depth of 85 m. Water was taken with a Niskin bottle and filtered on board directly using 5 μm and 0.2 μm polycarbonate filters. The indicated time represents the sampling time.We extracted DNA with a phenol-chloroform protocol (Klotz et al., 2021). We used the primer pair CamoA420F (50-CGT ACT GGT AGG AAT GTC-30; Herber et al., 2020) and CamoA616R (50-GCC ATC CAB CKR TAN GTC CA-30; Tourna et al., 2008), which are specific for the archaeal ammonia monooxygenase (amoA). The universal primer pair 1389F (50-TGY ACA CAC CGC CCG T-30) and 1492R (50-GGY TAC CTT GTT ACG ACT T-30; Hausmann et al., 2016) was applied to target the 16S rRNA gene of total Archaea and Bacteria. With this, we were able to gain absolute abundances of ammonia oxidizing archaea based on their functional marker gene amoA and relative abundances by comparing it to total Archaea and Bacteria abundances over a cycle of two years.