Heat shock proteins play an important role in protein homeostasis under stress conditions, and act as molecular chaperons in living organisms. Here, we investigate acute toxicity of heavy metals (Cu and Cd) and the transcriptional changes of the heat shock proteins (hsps) family genes (hsp20, hsp27, hsp70, hsp90α-1, and hsp90β) in Brachionus koreanus-exposed to heavy metals. As a result, 48-h LC50 values were 0.956 mg/L (95%-cl. 0.678–1.348) for Cu and 57.563 mg/L (95%-cl. 47.691-69.477) for Cd. The expressions of hsp90α-1 and hsp70 mRNA level at all concentrations were significantly upregulated 24 h after exposure to Cu and Cd. In particular, a significant increase in hsp27 and hsp70 mRNA level indicated higher sensitivity to Cd. This finding indicates that HSPs play protective roles under heavy metal stress in this species. In addition, the expression profiles of hsp27, hsp70, and hsp90α-1 may be useful as molecular marker for monitoring heavy metal toxicity in the aquatic environment.