This work is a part of research of rare Actinomycetal bacteria producing antimicrobial substances that may be used in agricultural, food and pharmaceutical fields. Among the 77 strains of actinomycetes isolated from different types of Moroccan ecosystems, 25 were selected according to their biological activity for molecular identification by sequencing the 16S rDNA fragment. After DNA extraction from isolates, amplification of 16S rDNA fragments by PCR technique (Polymerase Chain Reaction), sequencing of the amplified fragments and comparison of characteristic sequences obtained with the contents of a database and phylogenetic studies using special programs were used to develop phylogenetic trees of the twenty-five isolates. The results Analysis showed the taxonomic affiliation of all isolates to the genus Streptomyces and assign each of them to one or more species. This shows the abundance of this kind in relation to others in the studied ecosystems. While the absence of other types of actinomycetes can be explained either by the absence of these genera in these ecosystems, or by the isolation techniques used, or by the fact that microbial population in the sample is non-culturable. Thus, in the last case, the confirmation of the presence of other types in these ecosystems could be performed by amplification of the 16S rDNA PCR from DNA mixture obtained directly from samples.