The purse-seiners of the Java Sea use light and fish aggregating devices (FAD) to concentrate and catch small pelagic fish (Decapterus sp., Amblygaster sirm, Sardinella gibbosa). This sets a question about the interaction between fish and fishing vessels. Relevant estimates of fishing mortality and fishing effort require an understanding of this interaction. To gain information on this relationship, acoustic surveys were performed on the fishing grounds and the present paper analyses these data. Using acoustic surveys, the fish density was measured and the number of schools was counted per sea surface unit. The fishing vessels were located by radar. Acoustic data were stratified into two groups, one where fishing vessels were present and the other where they were not. This stratification was tested for by resampling the data. Day and night sampled data were analysed in each strata separately. Variograms were computed to characterise spatial structure both for the fish and the purse-seiners. Contingency tables between number of schools and fish density were computed to characterise the relation between biomass and schools for the day and the night when seiners are absent or present. At night, in the absence of purse-seiners, the number of schools increase and fish rise from the bottom. In areas where purse-seiners are present this natural phenomenon is stronger. It also changes the spatial structure both of the fish density and the school abundance. The spatial structure of the vessels is similar to that of the fish density. The fishermen seem to be able to detect by day fish concentrations which will be fished later by night.