With increasing population in the world, energy needs will also increase. The energy used in everyday life will usually be related to fossil fuels. Alternative fuels are needed as a solution to these problems, including Biodiesel. However, the use of Biodiesel still has problems in its resistance to oxidative degradation during storage. The double bonds in the Biodiesel molecule produce a high level of reactivity with oxygen, especially when placed in contact with air. As a result of the storage for a long time can cause degradation of fuel properties that affect the quality of Biodiesel itself. This research was carried out for 12 weeks with storage conditions in stainless steel tanks such as in fuel storage tanks that are commonly used. Variations for storage conditions are: (1) storage indoors at ambient temperature, (2) tanks stored on ships with coastal/marine air conditions with direct air circulation into tanks, (3) tanks stored on ships with conditions beach / sea air with air filters on the tank. To get the characteristics of molecular changes that occur as a result of variations in storage conditions, biodiesel testing is carried out with the FTIR test method. The results obtained show that at the beginning of the month there were peaks in the functional groups of carboxylic acid compounds and aldehyde acids with a delta transmittance of 9.48% at the beginning of last month decreasing to 9.4% in the third month for Low RH, whereas for High RH there was a peak with a transmittance delta of 10.91% at the beginning of last month, down to 9.48% in the third month. However, in the High RH condition there is a significant increase in the transmission delta. There was a peak in the functional group of carboxylic acid compounds with a delta transmittance of 17.57% at the beginning of last month, increasing to 31.3% in the third month. Likewise with the growth of aldehyde acid compounds which at the beginning of the storage month had a peak with a transmittance delta of 9.37% and an increase in the third month of 17.48%.