Background: Rhamnolipids is the most widely studied and applied biosurfactants. The anaerobic biosynthesis of rhamnolipids has important research and practical significance, such as meeting the in situ production of biosurfactant in anoxic environments and the foamless fermentation of biosurfactants. A few studies have reported the anaerobic biosynthesis of rhamnolipids from rare Pseudomonas aeruginosa strains. What did promote the anaerobic biosynthesis of rhamnolipids, the specificity of the rare strains or the effect of specific substrates? Here, anaerobic production of rhamnolipids by different P. aeruginosa strains was investigated using diverse substrates. The anaerobic biosynthesis mechanism of rhamnolipids were also discussed from the substrate point of view.Results: All P. aeruginosa strains anaerobically grew well using the tested substrates. But all P. aeruginosa strains anaerobically produced rhamnolipids only using substrates containing glycerol and nitrate. Fourier transform infrared (FTIR) spectra analysis confirmed the anaerobic production of rhamnolipids from all P. aeruginosa strains. All the anaerobically produced rhamnolipids decreased air-water surface tension from 72.6 mN/m to below 29.0 mN/m and emulsified crude oil with EI24 above 65%. Using crude glycerol as low-cost substrate, all P. aeruginosa strains can anaerobically grow and produce rhamnolipids to reduce the culture surface tension below 35 mN/m. The glycerol metabolic intermediate, 1, 2-propylene glycol, can also achieve the anaerobic production of rhamnolipids by all P. aeruginosa strains.Conclusions: Not the specificity of the rare P. aeruginosa strains but the effect of specific substrates promote the anaerobic biosynthesis of rhamnolipids by P. aeruginosa. Glycerol and nitrate are the excellent substrates for anaerobic production of rhamnolipids from all P. aeruginosa strains. Results indicated that glycerol metabolism involveed the anaerobic biosynthesis of rhamnolipids in P. aeruginosa. Results also showed the feasibility of using crude glycerol as low cost substrate to anaerobically biosynthesize rhamnolipids by P. aeruginosa.