At the end of the last century, bacterial biofilms were recognised as being a common cause of persistent infections. This finding encouraged intense research in biofilms, revealing that the biofilm life form is an essential factor for bacteria to develop persistent infections, which is because of an increased resistance to the immune system and conventional antibiotics. However, the increased scientific focus on studying the underlying mechanisms of biofilm formation has not yet led to the development of efficient therapeutic applications to eradicate biofilm infections, and treatment of these infections remains a critical struggle for physicians. The bacterial cell-to-cell quorum-sensing signalling system and the intracellular cyclic-di-GMP signalling system have gained increasing attention as potential targets for the treatment of persistent biofilm infections. Here, we describe these two systems in relation to virulence and regulation of biofilm formation in Pseudomonas aeruginosa. We also describe the potential use of small molecules to chemically interfere with these systems for treatment purposes, and we review the scientific development and novel findings of compounds that have been identified as potential modulators of the two regulatory processes.