Environmental change challenges local and global survival of populations and species. In a speciespoor environment like the Baltic Sea this is particularly critical as major ecosystem functions may be upheld by single species. A complex interplay between demographic and genetic characteristics of species and populations determines risks of local extinction, chances of re-establishment of lost populations, and tolerance to environmental changes by evolution of new adaptations. Recent studies show that Baltic populations of dominant marine species are locally adapted, have lost genetic variation and are relatively isolated. In addition, some have evolved unusually high degrees of clonality and others are representatives of endemic (unique) evolutionary lineages. We here suggest that a consequence of local adaptation, isolation and genetic endemism is an increased risk of failure in restoring extinct Baltic populations. Additionally, restricted availability of genetic variation owing to lost variation and isolation may negatively impact the potential for evolutionary rescue following environmental change.