Ectomycorrhizal (ECM) colonisation patterns and seedling growth of containerised spruce seedlings were studied in five typical Finnish forest nurseries by morphotyping and molecular characterisation. ECM colonisation degree of 1-year-old spruce seedlings was below 20% in all studied Finnish forest nurseries. In 2-year-old spruce seedlings the ECM colonisation degree was ca. 50–60% in three of the nurseries, but negligible in others. The ECM fungal species richness varied from 0.1 to 3.8 types per seedling. Altogether seven ECM morphotypes were distinguished. The clearest factors associated with ECM colonisation patterns were nitrogen and phosphorus fertilisation. Particularly fertilisation in the early stage of seedling development appeared to diminish the degree of colonisation and species richness of ECM fungi. Root/shoot ratio was positively correlated with high colonisation degree and species richness of ECM fungi. Higher fertilisation inputs in these overall fertilisation levels did not increase the size of the seedlings. According to these results moderate fertilisation levels particularly in the beginning of seedling cultivation are critical for generating higher root/shoot ratios and sufficient ECM colonisation degree of the roots.