We report on the first separation of a complex biomixture in pressure-driven mode using perfectly ordered pillar array columns. The separations were conducted in the reversed-phase mode using a highly aqueous mobile phase, while the outer surface of the non-porous pillars was chemically functionalized with a hydrophobic C8-layer. The samples originated from two different bacterial strains (Pseudomonas aeruginosa PAO1 and Pseudomonas sp. W15Feb38) of fluorescent pseudomonads. These produce fluorescent yellow-green pyoverdines that serve as siderophores to shuttle iron inside the cell. The pyoverdines of both strains were prepared from the supernatant through a crude solid phase extraction without any further purification step. In case of the PAO1 mixture, a separation of 15 components within a column length of 2.5 cm could be observed through the transparent cover glass of the chip. For the W15Feb38 mixture, a separation of eight components could be observed within the same distance. These fast chromatographic separations were compared with those obtained via iso-electrofocusing (IEF), which is the traditionally employed fingerprinting method to characterize pseudomonad strains based on their pyoverdine profiles (siderotyping). With this technique, and despite the injection of a 10,000 times larger sample mass, only nine bands were maximally observed for the PAO1 mixture, whereas maximally six bands were observed in case of the W15Feb38 mixture. The chromatographic pillar array method, yielding a separation in less than 1 min, was also significantly faster than the IEF method, which typically needs 1.5h. The present system can therefore be considered as a potential alternative fingerprinting tool for the fast identification of different strains of fluorescent pseudomonads, including as diagnostic tool for typing strains of the important opportunistic pathogen P. aeruginosa.