The effects of habitat degradation remain not fully understood. A recent study reported low effects of habitat degradation on plant genetic diversity but indicates that reduction in habitat quality could impact it as well as gene flow indirectly via ecological interactions. Selective logging is a way of habitat degradation, but studies examining its effects on plant genetic diversity on non-logged forest plant species are relatively scarce. Using 3470 single-nucleotide polymorphisms, we assess the effects of different selective logging intensities on the genetic diversity of 66 individuals of a keystone mistletoe (Tristerix corymbosus). We also examined the possible relationship with its seed disperser (Dromiciops gliroides) abundance in three sites of the temperate rainforests of southern Chile, with different levels of selective logging intensity. Our results show that selective logging increases allelic richness and inbreeding in this mistletoe; inbreeding increased with selective logging intensity, and heterozygosity decreased with D. gliroides abundance. While wood extraction seems to positively affect T. corymbosus genetic diversity, its long-term consequences—such as increased inbreeding—are yet to be assessed in future studies.