Oil content extraction from the rock pores can be very complicated due to the high viscosity of petroleum oil and low degree of reservoir rock porosity as well as its permeability. A research had been carried out with the use of mix populations of indigenous bacteria isolated from formation water (fw), wellsite sludge (ws) and well mud (wd). Limestones was used as samples. This cores were soaked for 2 (two) weeks in 55 0 C, a media contained of 1% molasse dissolved in sterillized formation water and 20% crude oil as covering. During the research, there was a change in the pH environment from neutral to acid. Acid production from the reaction result with carbonate in the solution will lower pH of the water that was produced. Changing value of porosity (%) that was injected by bacteria from fw, ws, and wd, increases respectively 23.22, 68.29, 14.89, and changing value of permeability (%) respectively 56. 28, 137.83, 35.77. Even though on average there were an increase in value of porosity and permeability, there were also a decrease in the value of porosity and permeability of a few of the limestones samples. Inoculum bacteria from the pollution around the oil well are much more adaptive and give more carbonate dissolving reaction than the other actions. MEOR (microbial enhanced oil recovery) technique is really dependent on the growth of the microbes in site, and the development of the secondary metabolit products that can change the porosity and permeability of the reservoir limestones.