CE-ESI-MS with a liquid sheath interface and IT mass analyzer was used for analysis of siderophores from different strains of Methylobacterium spp. citrus endophyte extracts. Three Methylobacterium strains were investigated according to positive bioassay tests. Bacteria cultures were grown under Fe(III) absence (siderophore producing cultures) and under Fe(III) presence (control cultures). Siderophores were extracted from culture supernatant with polystyrene resins. BGE and sheath-liquid composition were optimized, respectively, in order to assure both, best peak resolution and ESI-MS sensitivity. The best analysis conditions were obtained with 100 mmol/L ammonium bicarbonate at pH8 as BGE and methanol:H2O 25:75 + 0.05% formic acid as sheath liquid. CZE-ESI-MS analysis revealed two possible siderophores, according to bacterium species, presenting M-r of 1004.3 and 798.3 Da.