The 2014-2016 marine heatwave (MHW) significantly altered primary productivity, impacting kelp ecosystems and deep reef fishes. However, its effects on mesophotic (low-irradiance) sessile reef invertebrates remain unknown. Invertebrates support diversity and ecosystem functioning across California’s reefs, most of which lie in mesophotic depths, yet their responses to environmental variability remain unclear. We examined decadal trends and responses to the MHW in cold-temperate mesophotic benthic sessile invertebrate communities from 2005 to 2021 using remotely operated vehicle surveys across a five-degree latitudinal gradient. Community structure changed, with significant shifts across higher-latitude reefs (35.2°-39°). In the south (33.5°–34°), sponge abundance increased 3-fold, while gorgonians (red, purple, and California golden) declined by 58%. During this period, orange- and gray puffball sponge populations showed widespread increases, whereas red gorgonians in the north (37.7°-39°) exhibited the most pronounced reductions (-97.8%). Thermal conditions alone cannot explain the divergence in gorgonian patterns and assemblage structure, as MHWs at 80 m depth exhibited asynchronous oscillatory heating between regions. The lack of a marine protected area effect indicates that large-scale environmental forces overshadow potential protection benefits, driving long-term changes in sessile fauna on California’s mesophotic reefs. This underscores the need to account for broad-scale stressors in marine protected area management.