The assessment of microbiological hazards is established to evaluate the effect of HACCP pre-requisite programs implementation and the methods of dehydration on microbiological hazards in some medicinal and aromatic plants. Gap analysis had been established on three models of dehydration to assess the probability of HACCP pre-requisite programs implementation. One of these models was natural dehydration which was not hygienically illustrated and we couldn't apply to implement HACCP pre-requisite programs especially cleaning and disinfectant program. Others were solar and oven dehydration models which were good illustrated to apply HACCP pre-requisite program. The study compared the microbiological hazard among these models of dehydration of two deferent medicinal and aromatic plants which were Calendula (Calendula officinalis) and Chamomile (Matricariachamomilla). Swaps were taken from workers hands and products contact surfaces of each dehydration models. samples were collected from the dried plants of each models.All of these swaps and samples were transferred to microbiological laboratory directly to be tested for total aerobic bacterial count, coliform group, Staphylococcus aureus, Salmonella spp. and mold & yeast. Results of workers hand and products contact surfaces microbial swapsshowed a significant decrease (p≤0.05) in oven and solar dehydration respectively than natural dehydration. Also microbial test of dried products showed a significant decrease (p≤0.05) in oven dehydrationthan solar dehydration than natural dehydration.