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Acute bacterial conjunctival infections are common, and this study identified the conjunctival bacterial community in infectious conjunctivitis cases seen at the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. The study included 47 randomly selected patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constituted 92% of all sequences (<i>Firmicutes</i> (35%), <i>Actinobacteria</i> (31%), and <i>Proteobacteria</i> (26%)). At the genus level, there were 12 common genera that constituted about 61% of all sequence reads. Seven of those genera were common (<i>Streptococcus</i> (10%), <i>Cutibacterium</i> (10%), <i>Staphylococcus</i> (7%), <i>Nocardioides</i> (7%), <i>Corynebacterium</i> 1 (5%), <i>Anoxybacillus</i> (5%), and <i>Acinetobacter</i> (5%)), which encompassed 49% of all reads. As for diversity analysis, there was no difference on PERMANOVA analysis (unweighted UniFrac) for sex (<i>p</i> = 0.087), chemosis (<i>p</i> = 0.064), and unclassified eyedrops (<i>p</i> = 0.431). There was a significant difference in cases with bilateral conjunctivitis (<i>p</i> = 0.017) and for using antibiotics (<i>p</i> = 0.020). Of the predominant phyla, <i>Firmicutes</i> had the highest abundance in bacterial conjunctivitis in this study. <i>Pseudomonas</i> as a resident commensal microbiota may have an important role in the prevention of infection.