Mushroom is one of the major sources of β-glucan used in medical applications and traditional therapies. Thus, structure analysis and quantification of β-glucan content is crucial to evaluate medicinal mushrooms. Most studies concerning mushroom-derived β-glucan have been focused on β-1,3-glucans. However, recent investigations suggest that β-1,6 glucans have important roles for immunomodulating activity. Therefore, to elucidate the fine structure of various mushroom-derived β-glucans, we recently developed a novel β-1,6 glucan detection system using the function-modified recombinant β-1,6-glucanase. In this study, we performed an ELISA-like assay using modified β-1,6-glucanase and soluble dectin-1-Fc as the probes for β-1,6-glucan and β-1,3-glucan, respectively. Reactivity of ELISA to crude hot water extracts of edible mushrooms (Grifola frondosa, Agaricus bisporus, Pleurotus tuoliensis, P. eryngii, P. ostreatus, Hypsizygus marmoreus, and Lentinus edodes) was compared and L. edodes showed the strongest reactivity among them. An additional 19 different products of fresh L. edodes (shiitake mushroom) commercially available in Japan were also analyzed. This revealed limited differences in amounts of β-1,6-glucan and β-1,3-glucan in each shiitake mushroom. Furthermore, structural analysis of some purified β-glucans derived from medicinal mushrooms was performed, and their action for inducing tumor necrosis factor-α production from the murine bone marrow-derived dendritic cells was investigated. We found relation between reactivity to modified β-1,6-glucanase and its cytokine inducing activity. This assay could be useful for evaluating the strains of edible or medicinal mushrooms, which may be used as alternative medicines.