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The present study examined the genetic diversity and spatial distribution of turbot (<i>Scophthalmus maximus</i>), an economically important species on the Bulgarian Black Sea coast. Maximum entropy (MaxEnt) modeling software Version 3.4.4. was utilized to develop a habitat suitability model for <i>S. maximus</i> in the Bulgarian Black Sea region. Data collected via demersal and pelagic surveys and genetic sampling from 2017 to 2021 were utilized to link species occurrence localities with selected abiotic factors. Our findings showed that the species’ habitat preferences are strongly influenced by temperature and dissolved oxygen, and projections based on simplified climatic scenarios indicated potential distribution shifts and a substantial reduction in reproduction habitats in the northern region. The assessment of genetic diversity was based on mtDNA COIII sequencing; MtDNA revealed a low level of polymorphism in all analyzed populations. The extensive fishing pressure may have increased the likelihood of genetic and population bottlenecks and a consequent decline in genetic diversity in the Shabla, Nesebar, and Tsarevo populations. The Tajima’s D values for the latter indicated that turbot underwent a bottleneck followed by rapid population expansion. Our findings are essential for the conservation and effective management of <i>S. maximus</i> stocks in the region.