This letter presents a novel waveguide orthomode transducer (OMT) with integrated filters. Resonator‐based bandpass filters are used for the two channels forming a duplexing OMT. As an example, a two‐channel duplexing OMT is designed with channels at 9.9‐10.1 GHz and 10.9‐11.1 GHz. A good filter response with 20 dB return loss is achieved for both the channels. The upper and lower bands are isolated to −80 dB due to the filtering elements and a transmission zero. This new multifunction compact filter‐OMT design leads to the size reduction and improved inter‐band isolation. A CNC machined waveguide OMT is demonstrated and its performance is verified with excellent agreement between the electromagnetic wave (EM) simulation and measured results.