Different methods have been used to extract the Phospholipid Fatty Acids [PLFAs] from soil, sediments and microbial pure cultures. Even though based on similar chemical principles of extraction, a major difference between sceintific groups studying PLFAs across a diverse range of environmental samples have been in the methanol esterification step, where acid or base catalysis have been used. This leads to the  question about how standardised the method is for phospholipid fatty acid analysis carried out in different soils or sediments from the diverse ecological niches, and thereby the appropriateness of developing one common database for resuklts comparison. We performed a comparative analysis of PLFA concentrations extracted and methylated using an acid or base catalysis. Our results show a statistically significant and higher concentration of the fatty acid methyl esters resulting from acid catalysed methylation compared to the base catalyed precedure. The robustness of either of the catlysed reactions and the reaction effects on the fatty acid methyl ester concentrations adds a new dimesnion to the choice of methods for PLFA reserach from environmental substrates.