Ectomycorrhizal (EcM) fungi contribute significantly to the shaping of short-root morphology, playing an important role in balancing the costs and benefits of root growth and nutrient uptake and exchange in boreal forests. We aimed to assess the effect of various EcM fungal taxa on root traits at seven sites dominated by grey alder, Alnus incana (L.) Moench, and black alder, Alnus glutinosa (L.) Gaertn. Mean root size, specific root length, specific root area, root tissue density, and root-tip frequency of EcM short roots were measured in EcM anatomotypes in relation to the effects of host species, soil moisture level, and nutrient status. Redundancy analysis revealed that anatomotype, alder species, site, and soil parameters (N, P, K, Ca, and Mg concentrations, pH, organic-matter content) accounted for 42.3% (p < 0.001) of the total variation in EcM root morphology. Variation decreased in the following order: anatomotypes (27.9%) > soil parameters and sites (19.9%) > alder species (5.1%). EcM fungus species had the primary influence on EcM short-root size. EcM roots of the dominant anatomotype, Alnicola spp., had the highest specific root length and specific root area in both alder species. Short-root morphology depends most strongly on the fungal taxa involved, which indicates that the type of mycobiont has an important influence on the functional properties of fine roots.