The use of microorganisms to improve fuel quality has been proposed, and in this chapter we describe basic experimental procedures for the isolation and characterization of bacteria for biodesulfurization and biodenitrogenation with dibenzothiophene and carbazole as model compounds for each application, respectively. The presented protocols should be considered as a starting point and adapted to other problematic compounds and conditions. Basic protocols for the evaluation of the treatment of real oil fractions are also presented.