Flow cytometry has recently been introduced in aquatic ecology. Its un
ique feature is to measure several optical characteristics simultaneou
sly on a large number of cells. Until now, these data have generally b
een analyzed in simple ways, e.g., frequency histograms and bivariate
scatter diagrams, so that the multivariate potential of the data has n
ot been fully exploited. This paper presents a way of answering ecolog
ically meaningful questions, using the multivariate characteristics of
the data. In order to do so, the multivariate data are reduced to a s
mall number of classes by clustering, which reduces the data to a cate
gorical variable. Multivariate pairwise comparisons can then be perfor
med among samples using these new data vectors. The test case presente
d in the paper forms a time series of observations from which the new
method enables us to study on the temporal evolution of cell types.