Actinobacteria are a major source of bioactive secondary metabolites. Due to the resistance of several antibiotics by pathogenic bacteria, the search for new natural products becomes necessary. This study aimed to search for non-ribosomal peptides produced by actinobacteria isolated from Dark Earth soils of Brazilian Amazon region and their characterization. Actinobacterial strains were isolated from soil samples collected at 10, 30 and 50 cm depth. A total of 150 isolates were screened for antimicrobial activities. Five of them were selected for further studies. The isolates BCM20, BCM32, BCM41, BCM59 and BCM60 were grown in a specific liquid medium for 24 h at 28^oC. Genomic DNA was extracted and PCR amplification was carried out using specific primers for NRPS (MTF/MTR) and PKS (KSF/KSR). Extracellular metabolites were extracted from the culture media using ethyl acetate and chloroform followed by extracts concentration. Organic extracts were investigated for the presence of bioactive compounds, such as siderophores and antibiotics. The results showed that BCM59 presented NRPS, BCM32 and BCM60 presented PKS, while BCM20 and BCM41 showed both genes. BCM20 isolate exhibited inhibitory activity against Rhizobium sp CB1809 and Burkholderia sp 204b, and isolates BCM32, BCM41, BCM59 and BCM60 isolates inhibited Candida kruzeii. Siderophore production was observed in BCM20, BCM32 and BCM41 isolates. Mass spectrometry is been used to identify compounds. In conclusion, the detection of NRPS and PKS genes in these isolates suggest that they produce bioactive compound by a non-ribosomal pathway. The molecular approach used here showed to be useful for the search of novel secondary metabolites by actinobacteria.