Aims: Pseudomonas putida CP1 is an interesting environmental isolate which exhibits substrate-dependent autoaggregation when the organism was grown on 0.5% (w/v) fructose. Autoaggregation is a process of a single bacterial species to develop clumps of cells during a substrate stress. This study was carried out to investigate the genetic changes in the bacterium during aggregate formation. Methodology and results: P. putida CP1 was grown on 0.5% (w/v) fructose in batch culture at 30 °C and 150 rpm. The removal of fructose from the medium corresponded with aggregation of the cells which started after 8 h incubation. Microarray gene expression profiling using a P. putida KT2440 Genome Oligonucleotide Array (Progenika, Spain) showed that 838 genes involved in metabolism and adaptation were differentially expressed in P. putida CP1. Global transcriptomic profiling studies showed that P. putida CP1 growing on fructose resulted in the induction of genes encoding for proteins mainly involved in protein translation, ABC transporters, oxidative phosphorylation and two-component systems (TCS). Novel genes, associated with autoaggregation, were identified using transcriptomic analysis involved in ABC transporter, TCS, flagella assembly and lipopolysaccharide biosynthesis. It was also associated with the up-regulation of genes involved in the flagellar assembly including the fliE gene which encodes for the flagellar hook-basal body protein. Conclusion, significance and impact of study The identification of new genes involved in autoaggregation formation is important to understand the molecular basis of strain variation and the mechanisms implicated in cell-cell communication.