Evaluation of the impact of climatic changes on the composition of fish assemblages requires quantitative measures that can be compared across space and time. In this respect, the mean temperature of the catch (MTC) approach has been proven to be a very useful tool for monitoring the effect of climate change on fisheries catch. Lack of baseline data and deep-time analogues, however, prevent a more comprehensive evaluation. In this study, we explore the applicability of the mean temperature approach to fossil fish faunas by using otolith assemblage data from the eastern Mediterranean and the northern Adriatic coastal environments corresponding to the last 8000 years (Holocene) and the interval 2.58-1.80 Ma B. P. (Early Pleistocene). The calculated mean temperatures of the otolith assemblage (MTO) range from 13.5 to 17.3 °C. This case study shows that the MTO can successfully capture compositional shifts in marine fish faunas based on variations in their climatic affinity driven by regional climate differences. However, the index is sensitive to methodological choices and thus requires standardized sampling. Even though theoretical and methodological issues prevent direct comparisons between MTO and MTC values, the MTO offers a useful quantitative proxy for reconstructing spatial and temporal trends in the biogeographic affinity of fossil otolith assemblages.