Biodiesel is a biodegradable fuel which is used in many countries. One of the raw materials for biodiesel production is microbial oil. Microbial oils have a good potential in lipid productivity. Extracted lipid from Citrobacter youngae CECT 5335(T) was used for biodiesel production. Also, the effects of medium component and culture conditions on biomass and lipid production of C. youngae were studied. The ranges of studied parameters were: concentration of sugar cane as a carbon source: 4-10% (w/v), pH: 4-7 and temperature: 20-35 degrees C. Maximum lipid production was 12.95 g/l at 35 degrees C, pH of 7 and the cane concentration of 4% (w/v). Under the optimized condition, a biomass of 24 g/l and a lipid content of 53.9% could be achieved. By using this lipid and choline hydroxide as an ionic liquid catalyst, at 60 degrees C and 2.5 h of reaction time, biodiesel was produced. The yield of obtained methyl ester was 79.48%. The biodiesel properties were analyzed according to ASTM D6751. All measured properties fulfilled the biodiesel standard criteria. (C) 2015 Elsevier Ltd. All rights reserved.