Ecuadorian Amazon Region is known as one of the richest biodiversity environment worldwide. However, it is a fact that microorganisms biodiversity have been poorly studied. In order to contribute to unravel microbe biodiversity and applications, this research aimed to quantify and characterize native microorganisms associated with cocoa (Theobroma cacao) plantations under high cadmium levels in two contrasting Ecuadorian Amazon conditions (CIPCA and Ahuano). Soils samples were collected from two deeps levels (0-10 cm and 10-30 cm) to compare the number of bacteria and fungi in both environments assessed. For microorganisms quantification, decimal dilution methods was performed and most probable number was calculated. Bacteria biodiversity was assessed by isolation of every different single colony and morpho-cultural characterization was performed measuring: colour, growth, shape, elevation, edges, Gram stains and morphology. Fungi biodiversity was evaluated by mycelia shape, colour and radial growth. Results showed the increase in bacteria and fungi under CIPCA environment, where the rainy range was not so high. However, in both ecosystems from 10-30 cm deep, the number of microorganisms were remarkable as compared with 0-10 cm deep. Bacteria characterization highlighted a huge diversity, with 22 different isolates in CIPCA and 16 isolates in Ahuano. For fungi, the differences in morpho-cultural characteristics within both ecosystems were not wide, but also CIPCA had a high diversity with 25 different isolates as compared with 22 from Ahuano. These results are the base for further researches related with microbe applications, such as cadmium bioremediation.