Several advantages are gained by the use of granular sludge in wastewater treatment plants (WWTP), such as higher biomass retention, faster settling properties, lower energy costs and smaller operational land space. However, relatively few studies have been carried out on the biodegradation of recalcitrant pollutants in these systems, compared to research performed on conventional WWTP with floccular sludge. For instance, bioaugmentation of bacterial strains with metabolic abilities of interest in biological reactors for wastewater treatment has been intensively studied in conventional WWTP systems, but not in systems with granular sludge. In the project “Bioaugmentation and conjugative plasmid transference using bacteria from extreme environments to enhance biodegradation of recalcitrant pollutants in WWTP granular sludge”, funded by the Portuguese Foundation for Science and Technology, a group of bacterial strains showing potential capacity to metabolize recalcitrant pollutants (paracetamol, ibuprofen, fluoxetine and polyethylene terephthalate) was isolated and their genomes are being sequenced with the aim of identifying genes putatively involved in the metabolic pathways of interest. In addition, biodegradation experiments are being performed in laboratory-scale granular sludge bioreactors bioaugmented with selected isolates.