ANOSIM give you the P value (i.e. significance levels) and a R value (i.e. the strength of the factors on the samples). R value is supposed to vary between 0 and 1 (not between -1 and +1) but you can obtained negative values but they are always close to 0. R value close to 1 indicates high separation between levels of your factor (e.g. control vs treatment samples), while R value close to 0 indicate no separation between levels of your factor. Be careful with the significance level as it is express as %, so if you want the actual P value you have to divide by 100. ANOSIM (one-way) gives you 2 windows: one with the detail results and one with a graph (or 2 graphs if you perform two-way ANOSIM). The result window show you “TESTS FOR DIFFERENCES BETWEEN xx GROUP” which give you the overall P value and R value for your factor. Then you get the “Pairwise Tests” which give you the P values and R values for each level of your factors. For example if you have 1 control and 2 treatments in your factor, the pairwise tests will tell you if the samples from control and treatment 1 are significantly different (P value) and how strongly they are different from each other (R value), and will give you the same for control vs treatment 2, and treatment 1 vs treatment 2. The number of permutations you perform (Actual permutation) and the number you could perform (Possible permutations) are also given and are important. It help you to know if the ANOSIM is relevant in your case, by indicating if you could perform more permutations (you obtain more accurate P value) and if the number of possible permutations is low (e.g.