Crude oil is one of the most toxic pollutants in the ecosystems and exposure to its components can cause numerous alterations in organisms specially when mixed with chemical dispersant such as Nokomis 3F4. Here, we investigate changes in gut microbial community composition of Danio rerio adults exposed to the water accommodated fraction (WAF) of light crude oil and chemical enhanced WAF (CEWAF) with Nokomis 3F4 after 4 days of acute exposure. A metagenomic analysis (MiSeq platform) of the 16S rRNA gene of the intestinal microbiota was performed. Intestinal dysbiosis was found in exposed organisms when compared to the control group, with higher bacterial diversity and dominance in WAF exposed organisms. Observed changes included enriched abundances for Flavobacterium, Pseudomonas, Plesiomonas and diminished abundances for Aeromonas, Cetobacterium in WAF. Based on these results, we conclude that acute exposure to WAF and CEWAF of light crude oil generate dysbiosis in D. rerio.