With the ever increasing use of herbal medicines and the global expansion of the herbal medicines market, safety has become a concern for both health authorities and the public in many countries. This is because many contaminants and residues that may cause harm to the consumers have been reported. Many are natural such as naturally occurring radioxides, toxic metals, bacteria and fungi. Some arise from past and present use of agents or materials that pollute the environment and subsequently medicinal plants, such as emissions from factories or the residues of certain pesticides. For these reasons, there is currently a global danger to the health and well-being of the people. These risks can be reduced by ensuring that there is enough surveillance of herbal medicines so that those with harmful contaminants and residues above recommended limits do not reach the public. This study therefore was aimed at identification and characterization of the microbial contaminants in herbal medicines sold in Kenyan herbal clinics, Chemists, supermarkets and streets. The microbial loads were established and the contaminants isolated and identified.