Biodiversity–ecosystem function (BEF) research, particularly in terms of species and genetic diversity effects on primary productivity, has been a recent topic of interest. However, there is no known cases assessing interactive effects of both species and genetic diversity, where genetic aspects of multiple species are evaluated. This experiment utilizes the pool-Genotype-By-Sequencing method to quantify, rather than manipulate, genetic diversity of all component species on a plot population level. Experimental plots were constructed in the field under forest restoration conditions, each containing a population of 24 locally-collected saplings. Species diversity of pioneer species (Betula ermanii, Abies sachalinensis, Salix sachalinensis monocultures vs. all three polyculture) and presence of large mammal herbivores (fenced vs. non-fenced) were manipulated. Both increases in species diversity and genetic diversity resulted in reduced damage and increased productivity. Furthermore, genetic diversity affected species diversity effects on productivity and damage. Average genetic diversity of all component species in polycultures was positively correlated with complementarity effects on productivity. For damage, variation in genetic diversity of component species was negatively correlated with selection effects, and positively with complementarity and net species diversity effects. These results indicate a need to consider genetic diversity effects across multiple species in future BEF studies.