Cluster and principal component analyses of Toarcian-Aalenian microfossils from a uniform Fleckenmergel facies, found in two different parts of the Pieniny Klippen Basin have been undertaken on the basis of the percentage abundance of benthic foraminifers and the standardized number of all microfossils per 100-grams of sediment. The latter type of input data appeared to separate two paleobathymetric settings much better than relative benthic foraminiferal data alone. Comparison of the foraminiferal assemblages with fossil and recent analogues suggests not so strong paleodepth differences within the basin ranging from the middle/outer neritic for the Czorsztyn and the outer neritic and/or upper bathyal for the Branisko Zone. The shallower part of the basin is dominated by Spirillina associated with other epibenthic foraminifers, enhanced abundance of ostracods, crinoid and other echinoderm fragments. Higher abundance of crinoid fragments and sponge spicules within the shallower (Czorsztyn) zone suggests a slightly higher energetic environment with very weak bottom currents. Predominance of nodosariids associated with tubular agglutinated foraminifers (astrorhizids), as well as lower abundance of benthic foraminifers and ostracods linked to a higher abundance of radiolaria are supposed to indicate deeper basinal settings. These distributional trends are most likely related to trophic conditions, and only indirectly to the paleobathymetry of the basin.