Lactic acid bacteria strains Lactobacillus plantarum CWBI-B534 and Leuconostoc ssp. mesenteroïdes (L. mesenteroïdes) Kenya MRog2 were produced in bioreactor, concentrated, with or without cryoprotectants. In general, viable population did not change significantly after freeze-drying ( p>0.05). In most cases, viable population for cells added with cryoprotectants was significantly lower than those without ( p<0.05). Cellular fatty acids (CFAs) from the two strains in this study were analyzed before and after freeze-drying. Six CFAs were identified, namely, palmitic (C 16:0 ), palmitoleic (C 16:1 ), stearic (C 18:0 ), oleic (C 18:1 ), linoleic (C 18:2 ), and linolenic (C 18:3 ) acids were identified. Four of them, C 16:0 , C 16:1 , C 18:0 , and C 18:1 , make up more than 94% or 93% of the fatty acids in L. mesenteroides and L. plantarum, respectively, with another one, namely, C18:3, making a smaller (on average 5-6%, respectively) contribution. The C 18:2 contributed very small percentages (on average≤ 1%) to the total in each strain. C 16:0 had the highest proportion at most points relative to other fatty acids. Moisture content and water activity (a w ) increased significantly during the storage period. It was observed that C 16:1 /C 16:0 , C 18:0 /C 16:0 and C 18:1 /C 16:0 ratios for freeze-dried L. mesenteroides or L. plantarum, with or without cryoprotectants, did not change significantly during the storage period. According to the packaging mode and storage temperatures, C 18:2 /C 16:0 and C 18:3 /C 16:0 ratios for freeze-dried L. mesenteroides and L. plantarum with or without cryoprotectants decreased as the storage time increased. However, a higher C 18:2 /C 16:0 or C 18:3 /C 16:0 ratio for L. mesenteroides and L. plantarum was noted in the freeze-dried powder held at 4°C or under vacuum and in dark than at 20°C or in the presence of oxygen and light.Appl Biochem Biotechnol (2009) 157:70-84 DOI 10.1007/s12010-008-8240-