The different uses that are given to soils affect their physicochemical properties, which may have an effect on microbial communities. To determine these effects it must be understood how the different methods used in microbial ecology studies may affect the estimation of diversity. In the present study it was analyzed: 1) The effect of the ADN extraction (PowerSoil Kit vs Griffiths method) and the purification method (removing contaminants) and 2) the effect of land use in a conventional or agro-ecological way, in grazing systems and sugar cane crops in two regions of Valle del Cauca. The microbial communities were studied by the sequencing of the V4 region of the 16S rRNA gene by Next Generation Sequencing (MiSeq, Illumina).