Modern techniques involving molecular biology, such as metagenomics, have the advantage of exploiting a higher number of microorganisms; however, classic isolation and culture methods used to obtain antimicrobials continue to be promising, especially in the isolation of Actinobacteria, which are responsible for the production of many of these compounds. In this work, two methodologies were used to search for antimicrobial substances-isolation of Actinobacteria and metagenomics of the Atlantic Rainforest soil and of the cultivation of cocoa intercropped with acai berry in the Atlantic Rainforest. The metagenomic libraries were constructed with the CopyControl Fosmid Library kit EPICENTRE, resulting in a total of 2688 clones, 1344 of each soil sample. None of the clones presented antimicrobial activity against the microorganisms tested: S. aureus, Bacillus subtilis, and Salmonella choleraesuis. A total of 46 isolates were obtained from the isolation of soil Actinobacteria: 24 isolates from Atlantic Rainforest soil and 22 isolates from the intercrop cultivation soil. Of these, two Atlantic Rainforest soil isolates inhibited the growth of S. aureus including a clinical isolate of S. aureus MRSA-a promising result, since it is an important multidrug-resistant human pathogen.