Persulfide species present in mammalian cells play important toxicological roles against oxidative stress and methylmercury. Cystathionine γ-lyase (CSE) and cystathionine β-synthase (CBS) are enzymes that produce persulfide species using cysteine as a substrate in the presence of vitamin B₆. However, little is known about the regulatory mechanisms underlying the expression of these enzymes. In the present study, we searched for molecular probes from a library of 27 zinc complexes to analyze the mechanisms in vascular endothelial cells. We found dichloro(1,10-phenanthroline)zinc(II), termed Zn11, as a zinc complex that suppressed endothelial CSE expression without any change in CBS expression. This zinc complex can be used as molecular probes to analyze the regulation underlying endothelial CSE expression.