To investigate the effects of two natural compounds-containing mouthrinses (NCCMs) (a fructus mume (FM) extract-containing mouthrinse and an essential oil (EO)-containing mouthrinse) on gingival health and microbial profiles in young orthodontic patients. This 6-month randomized, single-blinded, parallel-controlled clinical trial consists of 90 patients with fixed appliance treatment. The subjects were allocated to (1) negative control group: oral hygiene instruction (OHI) alone; (2) test group 1: OHI plus EO mouthrinse; and (3) test group 2: OHI plus FM mouthrinse. Clinical examinations included plaque index (PI), bleeding index (BI) and modified gingival index (MGI). Salivary microbial quantifications included total aerobic and anaerobic bacteria, Streptococci and Lactobacilli counts. Clinical and microbiological examinations were conducted at baseline, 3rd and 6th months (T1, T2, and T3). BI was significantly reduced in both the FM mouthrinse and EO mouthrinse groups compared with the negative control group at T3 (P < 0.05). There were no significant intergroup differences in salivary bacteria counts in all groups (P > 0.05). Both NCCMs effectively reduced gingival bleeding without causing significant alterations of microbial profile in young orthodontic patients.