This manuscript describes the male genital tract microbiota and the significance of it on the host's and his partner's health. Microbiota exists in male lower genital tract, mostly in urethra and coronal sulcus while high inter-subject variability exists. Differences appear between sexually transmitted disease positive and negative men as well as circumcised and uncircumcised men. Upper genital tract is generally germ-free, except in case of infections. Prostatitis patients have frequently abundant polymicrobial communities in their semen, expressed prostatic secretion and/or post-massage urine. Coryneform bacteria have ambivalent role in male urogenital tract being frequently commensals but sometimes associated with prostatitis and urethritis. Interactions between male and female genital tract microbiota are highly likely yet there are very scarce studies on the couples’ genital tract microbiota. Increase of bacterial vaginosis-type microbiota and coliforms are the most typical findings in men while the adverse effect of male genital tract bacteria on in vitro fertilization and pregnancy outcome has also been indicated.