The identity of individual ectomycorrhizas, root colonization patterns and early growth responses of interconnected Scots pine (Pinus sylvestris L.) seedlings were investigated following interactions between local genets of Suillus bovinus (L. ex Fr.) O. Kuntze (SBK4b and SBK5b) and S. variegatus (Swartz ex Fr.) O. Kuntze (SVK3b) and different host–genotype combinations. Three equidistant 39-d-old seedlings, in pots that contained sterile N-limited nursery soil, were each inoculated with one of the three genets in the multiple inoculation treatment (MIT). Single inoculation treatments (SITs), involving inoculation of only one seedling in the triad with one of the three genets, and a similarly configured uninoculated treatment (UIT), were also prepared for comparative analysis. All seedling roots in the inoculated treatments, except for one SIT/SBK4b combination, hosted large numbers (>150) of Suillus-type ectomycorrhizas after 23–25 wk growth without additional fertilization. Esterase (EST) isozyme analysis of individual ectomycorrhizas from all SIT and MIT combinations enabled efficient interspecific and intraspecific typing of fungal (genet) colonization (89 and 72%, respectively) and identification of host genotype variation (Z locus polymorphism) at a lower rate (51%). Species, but not S. bovinus genet, typing within randomly sampled individual ectomycorrhizas from selected SITs was successful (50–70%) following PCR/RFLP analysis of diagnostic sequences of fungal rRNA genes. In the SITs, only the inoculated fungal genet was detected in ectomycorrhizas on all three seedlings. Roots were predominantly colonized by SBK4b in one, and SBK5b in three, of the MIT combinations, although ectomycorrhizas of the former genet were detected at low frequencies on nearly all seedlings. In the remaining MIT combination, both SBK4b and SVK3b were found to co-dominate as ectomycorrhizas on the seedling roots. Small numbers of the latter genet were detected in ectomycorrhizas of two SBK5b-dominated MIT combinations. However, no significant trends in host-mycorrhiza interactions were detected using a log–linear analysis. Compared with the UIT, significant positive mycorrhizal plant growth responses, particularly increased needle length, were recorded in all the heavily colonized seedlings in most SIT and all MIT combinations. Intermediate seedling growth was restricted to the one SIT/SBK4b combination where seedlings supported limited numbers of ectomycorrhizas. The general host-fungal colonization patterns observed provide further below-ground evidence supporting genet interactions previously detected through sporocarp population analyses in young Scots pine reforestation sites.