The anaerobic oxidation of methane (AOM), primarily driven by anaerobic methanotrophic (ANME) archaea, plays a crucial role in consuming sedimentary methane, particularly at marine cold seeps. In Monterey Bay, CA, numerous seeps have been identified and studied for many decades, but the indigenous microbial communities have not been characterized. Here, sediment cores were sampled along a distance gradient at two Monterey Bay cold seeps – Clam Field and Extrovert Cliff. We combined porewater geochemical measurements with deep amplicon sequencing of 16S rRNA and mcrA (DNA and RNA), and droplet digital PCR of mcrA genes and transcripts. One of the two seep sites contained negligible ANME signatures in our deep-sequencing datasets, despite methane and sulfide profiles typical of other cold seeps that host AOM, and despite 13C-DIC depletion with sediment depth. Subsequent microscopy and incubation experiments substantiated the ANME deficiency. We postulate that non-methane hydrocarbon release perturbs seep communities, potentially disrupting the normal methane oxidation process and permitting methane to accumulate. Our findings have implications for carbon cycling in the deep sea and raise concerns about methane release from marine sediments. Understanding the factors governing methane oxidation in cold seep environments is critical for assessing the global methane budget and its impact on climate change.