The aim of this study is to examine some bacterial genus in the oral microbiota of athletes and sedentary individuals. Fifteen male volunteers aged 18-24 participated in the study and they were divided into 3 groups. The first group consisted of male athletes playing football in the professional league (n=5), the second group consisted of male athletes playing football in the amateur league (n=5) and the third group who did not active any physical activity (sedentary) males (n=5). Groups were informed about the study before the measurement, informed volunteer consent form and demographic information form were applied. A oral swab sample was taken for the participants' oral microbiota measurements. Bioinformatics were analyzed the samples taken in Microbiology and Microbiota Analysis Laboratory by using Illumina MiSeq analyzer using the Next Generation Sequencing (NGS) method. In the analysis of the data, the significance level was taken as p<0.05 using the SPSS 24 software package. In addition, the microbial community profiles obtained were compared with each other and dendrograms were created using the Minitab 17 software. In the oral microbiota analysis of the groups, the dominant bacterial genus: Prevotella, Lachnospiraceae, Haemophilus, Leptotrichia and Streptococcus were found in the oral cavity. Lachnospiraceae and Streptococcus types of bacterias were found to be higher in the sport groups (professional and amateur footballers) than the sedentary group, and there was a statistically significant difference found between them (p<0.05). Furthermore, although the Prevotella and Leptotrichia types of bacterias found in the groups of athlete were less than the sedentary individuals and the Haemophilus type of bacteria of the professional footballers were higher than the other groups, there was no statistically significant difference (p>0.05). As a result; it can be said that football training performed both at a professional and amateur level may affect the important bacterial species in the oral microbiota of athletes. The fact that Streptococcus type of bacteria, which plays an important role especially in dental caries and infective endocarditis, is found more in the professional group may be related to the intense training which eventually may lead to the impairment of the oral microbiota. In the results, the oral microbiota of the group of athletes was associated with poor oral health. It has been a specific study by establishing the first relation of the subject related to the examination of oral microbiota diversity between athletes and sedentary groups at a taxonomic level.