Abstract: Methods and systems for automated counting and classifying microorganisms. A method disclosed herein includes receiving and analyzing quality of at least one input media of at least one incubated dish used for growth of the colonies of the microorganisms. The method further includes detecting the colonies of the microorganisms in a growth medium disposed on the dish if the received at least one media is a good quality media, wherein the detected colonies include at least one of individual colonies and grouped colonies. The method further includes segregating the grouped colonies into the individual colonies. The method further includes classifying the individual colonies into at least one species of the microorganisms. The method further includes counting the colonies of each species.