Ichthyofauna distribution and habitat characteristics of Thalassia beds in the Grand Cul-de-Sac marin lagoon in Guadeloupe were studied during a one-year survey. Environmental variables (9) were measured monthly in ten sites along with collection of fish communities. The environmental data set, analysed alone through between–within group ‘principal component analysis’ (PCA), exhibited a significant spatial and temporal variability. The fish data set, however, presented only a significant spatial structure, stable over the year. Given the lack of temporal variability in fish distribution, a ‘between-site co-structure analysis’ (BSCA) was used to compare the faunistic and environmental structures in space. The co-inertia structure was reduced to one axis representing a strong coast-reef gradient, the major common phenomena to both data sets. Environment and fish distribution allowed to distinguish sites directly under mangrove influence (characterised by high seagrasses, high concentration of chlorophyll a and high densities of zooplankton), to sites under reef influence (with short but dense seagrasses, clear water, and poor nutriments). For that purposes, the BSCA summarised efficiently what in common the fauna spatial structure and the environment spatial structure may present.