Forests are profoundly influenced by the rapid increase in nitrogen (N) deposition. Fungal communities dominate the decomposition of recalcitrant carbon (C) in soils, but it is still unclear how fungal communities respond to N addition in forests with different mycorrhizal associations. Here, we used the high-throughput sequencing methods to examine the effects of 16-year N addition on fungal diversity and community structure in two plantations, i.e., Dahurian larch (Larix gmelinii) associated with ectomycorrhiza and Manchurian ash (Fraxinus mandshurica) associated with arbuscular mycorrhiza, in Northeast China. We found that fungal alpha diversity was comparable between the two plantations and responded insignificantly to N addition. The permutational multivariate analysis of variance demonstrated that the fungal community structure was significantly affected by tree species, while N addition altered the fungal community structure in ash stand but had little effect on it in larch stand. The distance-based redundancy analysis further revealed that N addition regulated the fungal community structure dominantly by increasing N availability, while tree species influenced it mainly by altering soil labile C fractions. In addition, the fungal community structure was correlated with the activity of phenol oxidase. Overall, the effects of N addition on soil fungal communities in the forest ecosystems are tree species-specific, and N addition may decrease the ligninolytic capability through adjusting the fungal community structure.