There is always population surge towards physical market because it is a major outlet for purchase of food items and other human needs. Biological contamination of air is one of the serious issues of the environment varying among geographic areas and sampling heights. The aeromycology of three major markets in Warri metropolis which include Effurun market, Igbudu market and Main market using open plate method was evaluated. The study was conducted for the period of six (6) months (April to September, 2017) at two heights: human height (1.5m) and building height (3.5m) and three different locations (foodstuffs, clothing and abattoir sections) in each of these markets. Petri dishes containing PDA medium were exposed for 5 mins and incubated in the laboratory for 2–3 days. Developed fungal colonies were counted and sub-cultured to fresh PDA medium for identification by morphological and microscopic examination using standard identification keys. A total of 6145 colonies with 35 species were isolated and identified. Main fungi identified with their percentage frequency of occurrence include Aspergillus niger 699(11.37%), Mucor mucedo 459(7.47%), Penicillium candidum 404(6.57%), P. digitatum 395(6.43%), Monilia sp 324(5.27%) among others. Off these fungi, members of the Deuteromycotina contributed 46.58%, Ascomycotina 38.76% and Zygomycotina 14.66%. The population of fungal colonies varied from month to month as follows: July>August>June>September>May>April. Human height has 4285(60.73%) colonies while building height was 1860(30.27) colonies. Igbudu market, Main market and Effurun market have 2412, 2030 and 1702 fungal colonies respectively. There are strong indications that these market environments are heavily contaminated with airborne fungal spores which may pose a serious threat to food security and human health. Continuous clean-up exercise of these markets is imperative.