The rate of polyphosphate accumulation in extraradical hyphae of an arbuscular mycorrhizal fungus was investigated by conventional histochemistry and a new enzymatic method using a bacterial enzyme, polyphosphate kinase. Marigold (Tagetes patula cv. Bonanza Orange) was inoculated with Archaeospora leptoticha and grown under P-deficient conditions. Extraradical hyphae were harvested at 0, 1, 3 and 24 h after 1 mm P-application. PolyP levels were assessed by both metachromasy of Toluidine blue O and polyphosphate kinase which converted polyP to ATP followed by the ATP-luciferase assay. Percentage of hyphae with metachromatic granules was increased from 25 to 44% from 0 to 1 h, and a maximum of 50% was reach by 3 h. Polyphosphate content was doubled from 1 to 3 h after P-application (4.8–10.0 mol as Pi mg−1 protein) at a rate of 46.4 ± 15.1 nmol min−1 mg−1. The rate of polyphosphate accumulation in the hyphae was surprisingly rapid as those of polyphosphate-hyper accumulating microorganisms. The enzymatic method employed in the present study allows highly specific and sensitive assessment of polyphosphate in the mycorrhizal system.