Over three-quarter of the world’s population is using herbal medicines with an increasing trend globally. Plant medicines may be beneficial but are not completely harmless. The aim of this study is to evaluate the antimicrobial activity of different types and part of lemon against different microbial isolates. The antimicrobial effects of aqueous extracts of peel and juice from fresh and dried citrus and sweet lemon against 6 Gram-positive and 8 Gram-negative bacterial and one yeast isolates, including Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes, Enterococcus faecalis, Streptococcus pneumoniae, Streptococcus agalactiae, Pseudomonas aeruginosa, Enterobacter aerogenes, Klebsiella pneumoniae, Escherichia coli, Salmonella Typhi, Proteus spp., Moraxella catarrhalis, Acinetobacter spp. and Candida albicans, all of them were studied. The water extracts of all the materials screened showed various inhibitory effects. The juice of Citrus limon has antimicrobial activities more than other types of extracts. Escherichia coli, Staphylococcus epidermidis, Streptococcus agalactiae and Candida albicans showed the highest resistance to these extracts. Lemon species might have antimicrobial activity against different Gram-positive, Gram-negative and yeast pathogens and could be used for prevention of various diseases caused by these organisms.