The potential benefits of inoculation with AM (arbuscular mycorrhizal) fungi were investigated on Atlas Cypress (Cupressus atlantica G.), an endemic Cupressacea in Morocco. The parameters under study were (i) the growth of the plant, (ii) the functional diversity of soil microflora and (iii) the rock phosphate (RP) solubilizing activity. C. atlantica growth was measured after 12 months of culture in plastic bags arranged in a randomised complete block design with 10 replicates per treatment. Fungal inoculation consisted of either Glomus intraradices alone or a mixture of native AM fungi. P amendment was supplied under the form of Khouribga Rock Phosphate (KRP) powder. Microbial catabolic diversity was assessed by measuring CO2 production of SIR (substrate induced respiration) responses. Results showed that: (i) the fungal symbionts were effective to improve the growth of C. atlantica, confirming the requirement of mycorrhizal symbiosis for the successful establishment of C. atlantica in a degraded soil; (ii) G. intraradices appeared to be the most effective in promoting growth of C. atlantica, whereas indigenous AM fungi were relatively ineffective. Native AM fungi inoculation strongly modified functional abilities of the soil microflora, and in the treatments with P amendment, growth stimulations of native AM fungi inoculation were significantly higher than those of G. intraradices inoculation for the shoot growth and leaf P content; (iii) C. atlantica plants inoculated with native AM fungi could mobilize P from KRP more efficiently than those mycorrhized with G. intraradices. A strong interaction between KRP amendment and fungus inoculation was detected for the leaf P content results. In conclusion, the use of a mixture of native AM fungi combination may increase the chance of including one very effective fungal isolate, but also, creates a more favourable environment for the development of ecosystems processes.