This paper presents data from an investigation of the Late Miocene-Pliocene siliceous microfossils (diatoms and chrysophycean stomatocysts) from borehole V-466, east of the city of Bitola, southern Macedonia. The diatom flora consists of 127 species, varieties, and forms of diatoms of thirty genera, eighteen families, five orders, and two classes. Four associations are distinguished in the development of the diatomaceous flora, as confirmed by cluster analysis. Ecological data for the diatom taxa and the frustule/chrysophycean stomatocysts ratio are used in an attempt to reconstruct in detail the paleoecological conditions at the time of sediment deposition in detail.