Rhizosphere and endophytic bacteria are well known producers of siderophores, organic compounds that chelate ferric iron (Fe3+), and therefore play an important role in plant growth promotion in metalliferous areas, thereby improving bioremediation processes. However, in addition to their primary function in iron mobilization, siderophores also have the capacity to chelate other heavy metals, such as Al3+, Zn2+, Cu2+, Pb2+ and Cd2+, that can affect homeostasis and the heavy metal tolerance of microorganisms. The main goal of our study was to select the most efficient siderophore-producing bacterial strains isolated from the roots (endophytes) and rhizosphere of Betula pendula L. and Alnus glutinosa L. growing at two heavy metal contaminated sites in southern Poland. Siderophore biosynthesis of these strains in the presence of increasing concentrations of Cd2+ (0, 0.5, 1, 2 and 3 mM) under iron-deficiency conditions was analysed using spectrophotometric chemical tests for hydroxamates, catecholates and phenolates, as well as the separation of bacterial siderophores by HPLC and characterization of their structure by UHPLC-QTOF/MS. We proved that (i) siderophore-producing bacterial strains seems to be more abundant in the rhizosphere (47%) than in root endophytes (18%); (ii) the strains most effective at siderophore synthesis belonged to the genus Streptomyces and were able to secrete three types of siderophores under Cd2+ stress: hydroxamates, catecholates and phenolates; (iii) in general, the addition of Cd2+ enhanced siderophore synthesis, particularly ferrioxamine B synthesis, which may indicate that siderophores play a significant role in tolerance to Cd2+ in Streptomyces sp. •Identification and selection of the most efficient siderophore-producing bacterial strains.•Siderophore biosynthesis in the presence of increasing concentrations of Cd2+.•Analysis of different types of siderophores: hydroxamates, catecholates and phenolates.•Separation of bacterial siderophores by HPLC and characterization of their structure by UHPLC-QTOF/MS.