A comparative analysis of the structural organization and efficiency of the arbuscular mycorrhiza (AM) of the Medicago lupulina initial (mleam-7) and the mutant line (mlelam-6) lines, characterized by semy-dwarf pheno-type and abortive arbuscules and vesicules, was carried out in vegetation experiment with two modes of inoculation by Rhizophagus irregularis. The first mode is the inoculation by mycorrizal roots and second – by mycorrizal seedlings. Mycorrhizal roots of initial and mutant lines were analyzed using light microscopy. The efficiency of plant mycorrhization was estimated by yield of straw and by phosphorus (Р) content in shoots compared to control (plants without AM). In the experiment with mutant and inoculation by replanting mycorrhizal seedlings, the obligate symbiotrophic fungus ability to colonize the root cortex by intercellular hyphae with a low ability to form arbuscules was shown. This indicates the ability of AM fungus to absorb carbohydrates from the apoplast without the participation of arbuscules. The formation of AM in the mutant did not affect the growth of plants and the total P content in the shoots under both methods of inoculation. Defects in the regulation system of AM symbiotic activity and weak development of arbuscules and vesicles indicate the inability of the mutant to form full-f ledged arbuscocytes. The formation of AM in initial line mleam-7 favour the increase of shoots yield and P content in shoots compared to control (plants without AM). Moreover, judging by the shoots yield, the efficiency of AM inoculation by replanting mycorrhizal seedlings was significantly higher than by mycorrhizal roots. The obtained data indicate the possibility of regulating the ecological efficiency of AM in highly mycotrophic plants by selection of the optimal inoculation conditions.