Oral viridans streptococci are a reservoir of resistance genes for pathogens. Through prolonged exposure, long-acting macrolides (e.g., azithromycin) may induce the resistance of the commensals to macrolides more frequently than macrolides with a shorter half-life (e.g., clarithromycin). In a prospective, randomized, evaluator-blinded trial in healthy volunteers receiving standard courses of either azithromycin (n = 20) or clarithromycin (n = 20), we compared the susceptibility of oral viridans streptococci to macrolides over a period of 12 weeks. There was a significant temporal increase in the numbers of resistant isolates in both groups (p < 0.0005 at week 1). The proportion of macrolide-resistant isolates over time was significantly higher following azithromycin treatment (p = 0.0005), but returned to baseline values until week 12 in both groups. Temporal differential effects of azithromycin and clarithromycin on the induction of resistance were observed and need to be investigated regarding their effect on co-colonizing pathogens.