A novel series of thiepine derivatives were synthesized and evaluated as potential antimicrobials. All the synthesized compounds were evaluated for their antimicrobial activities in vitro against the fungi Candida albicans (ATCC 10231), C. parapsilosis (clinical isolate), Gram-negative bacterium Pseudomonas aeruginosa (ATCC 44752), and Gram-positive bacterium Staphylococcus aureus (ATCC 25923). Synthesized compounds showed higher antifungal activity than antibacterial activity indicating that they could be used as selective antimicrobials. Selected thiepines efficiently inhibited Candida hyphe formation, a trait necessary for their pathogenicity. Thiepine 8-phenylbenzothiepino[3,2-c]pyridine (16) efficiently killed Candida albicans at 15.6 μg/mL and showed no embryotoxicity at 75 μg/mL. Derivative 8-[4-(4,5-dihydro-1H-imidazol-2-yl)phenyl]benzothiepino[3,2-c]pyridine (23) caused significant hemolysis and in vitro DNA interaction. The position of the phenyl ring was essential for the antifungal activity, while the electronic effects of the substituents did not significantly influence activity. Results obtained from in-vivo embryotoxicity on zebrafish (Danio rerio) encourage further structure optimizations. This article is protected by copyright. All rights reserved.