Quality design of websites implies that among other factors, hypelinks’ structure should allow the users to reach the information they seek with the minimum number of clicks. This paper utilises the fuzzy equivalence relation based clustering in adapting website hyperlinks’ structure so that the redesigned website allows users to meet as effectively as possible their informational and navigational requirements. The fuzzy tolerance relation is calculated based on the usage rate of hyperlinks in a website. The equivalence relation identifies clusters of hyperlinks. The clusters are then used to realocate hyperlinks in webpages and to rearrange webpages into the website structure hierarchy.