This study analyzed the interaction between the small-scale fishers and the Mediterranean Monk Seal (MMS) in an important Peninsula and two important marine protected areas on the southwest coast of Turkey. The survey was carried out from January 2014 to December in 2015 in the Muğla Province. Small-scale fishers in the study sites were interviewed to assess the interactions between small-scale fishers and the MMSs including total economic loss of fishers from MMSs, the number of MMS sightings, the reactions of the seals and the fishers during the sightings, fishers’ perceptions on the MMS, and demographic and socio-economic profiles of the fishers. Small-scale fishers from Bodrum appeared to be the group that suffered the most among the locations with an annual loss of $1465.4 in contrast with Datça fishers with the lowest annual loss ($397.6). The annual loss in Fethiye-Göcek ($860.4) was almost double the loss of Bozburun fishers ($492.4). Harvesting costs varied from $6.7 kg^-1 in Bodrum to $14.5 kg-1 in Fethiye-Göcek, whereas it was $11.8 kg-1 in Datça and $8.8 kg-1 in Bozburun. In conclusion, small-scale fishers should be subsidized to cover their economic losses caused by MMSs. Furthermore, re-regulating and minimizing the relation between fishing areas and MMS habitats, and raising the awareness of the fishers about the MMS can be essential in minimizing the negative interactions. We also recommend the use of economic indicators such as DPUE rather than absolute values to better understand and illustrate the negative economic impacts of MMSs.