Tree harvesting practices that enhance genetic diversity are essential for the long-term sustainability of our forests. Using eSSRs, which are markers within expressed genes and thus, potentially subjected to natural selection and reveal adaptive potential, this study examines the effects of selection (SE) and shelterwood (SW) management systems using unmanaged (UM) stands as reference on the genetic diversity of sugar maples in the Northern Forest, USA. Comparison between management types shows no difference between SE and SW, but compared to UM, both have lower allelic richness (AR) while only SE has lower expected heterozygosity (HE). Size class comparison shows that seedlings have higher AR and HE than poles and mature trees. Two-way interactions between management types, size classes, and study stands from each of the four states that comprise the Northern Forest region (Maine, New Hampshire, Vermont and New York) were also examined. Results show that seedlings in UM and SW have higher AR compared to all size classes in SE and poles and mature trees in SW, while only seedlings from SW have higher HE compared to poles and mature trees in SE and SW. Only in Maine was there a difference in AR between SW and SE stands per state. Seedlings in New Hampshire and Maine have higher HE, as well as seedlings and mature trees in New York compared to the poles in New Hampshire and mature trees in Maine. Overall, the results indicate genetic erosion in sugar maple stands in the Northern Forest region. This genetic impact may be due to several factors including the intensity of cutting associated with SE and SW systems and size of the canopy gaps created. Higher seedling genetic diversity in SW compared to SE may be due to their more open stand structure that facilitates gene flow and seedling recruitment. When using SE, longer cutting cycle paired with lower level of residual basal area is recommended. This approach allows for a more open stand structure that could facilitate pollen and seed exchanges from the stands, improving their genetic diversity. In both SE and SW systems, leaving high-quality growing stocks will enhance their genetic diversity and ensure their sustainability. This study increases our awareness of the potential genetic impacts of forest harvesting practices and guides the development of recommendations to alleviate genetic erosion in sugar maple stands.