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<i>Chlamydia trachomatis</i>, a parasitic intracellular bacterium, is a major human pathogen that causes millions of trachoma, sexually transmitted infections, and pneumonia cases worldwide. Previously, peptidomimetic inhibitors consisting of a hydrophobic dipeptide derivative exhibited significant inhibitory effects against chlamydial growth. Based on this finding, this study showed that both bortezomib (BTZ) and ixazomib (IXA), anticancer drugs characterized by proteasome inhibitors, have intensive inhibitory activity against <i>Chlamydia</i>. Both BTZ and IXA consisted of hydrophobic dipeptide derivatives and strongly restricted the growth of <i>Chlamydia</i> (BTZ, IC₅₀ = 24 nM). In contrast, no growth inhibitory effect was observed for other nonintracellular parasitic bacteria, such as <i>Escherichia coli</i>. BTZ and IXA appeared to inhibit chlamydial growth bacteriostatically via electron microscopy. Surprisingly, <i>Chlamydia</i>-infected cells that induced a persistent infection state were selectively eliminated by BTZ treatment, whereas uninfected cells survived. These results strongly suggested the potential of boron compounds based on hydrophobic dipeptides for treating chlamydial infections, including persistent infections, which may be useful for future therapeutic use in chlamydial infectious diseases.