Abstract Microbial enhanced oil recovery has appeared recently as an alternative to obtain better performances in oil production. The new alternative needs detailed studies about the ability and capacity of bacteria associated with formation waters, or with percolated/injected waters during secondary crude oil recovery. In the present work, we analyzed the morphological characteristics and ability to use organic substrates of bacteria. Bacteria were isolated from water associated with some shallow, biodegraded oil wells, with average pressure of (falta) and temperature of 60°C, located on the Eastern Coast of Maracaibo Lake. Aliquot samples of 14 oil wells were taken, incubated at 32°C and 50°C during 15 days in mineral media supplemented with yeast and glucose extracts for bacteria recovery. A total of 150 colonies was isolated and their micro-macro morphology were observed; also 16 biochemical tests were performed accordingly with the particular characteristics of origin of these bacteria, grouped in sugar fermentation, protein hydrolysis, mineralization of nitrogen and phosphorous compound, high NaCl concentrations, and presence of haemolotical and amilolitical enzymes. These tests allow knowledge of the ability of bacteria to produce metabolites that improve crude oil recovery. Statistical grouping tests were performed to classify the bacteria in toxonomic and morphological groups, and their presence and abundance in each analyzed oil well. The bacterial colonies formed seven groups, with non-homogenous distribution in the different oil wells. The results suggest that the source of the bacterial groups are not the same, or their presence in the oil wells do not have a common origin; this study also allows us to know the kind of energetic resource that must be used in each particular oil well.