Systemic risks have to be vigilantly guided against at all times in order to prevent their contagion across stock markets. New policies also may not work as desired, instead even induce shocks to market, especially those emerging ones. Therefore, timely detection of systemic risks and policy-induced shocks is crucial to safeguard the health of stock markets. In this paper, we show that the relative entropy or Kullback-Liebler divergence can be used to identify systemic risks and policy-induced shocks in stock markets. Concretely, we analyzed the minutely data of two stock indices, the Dow Jones Industrial Average (DJIA) and the Shanghai Stock Exchange (SSE) Composite Index, and examined the temporal variation of relative entropy for them. We show that clustered peaks in relative entropy curves can accurately identify the timing of the 2007–2008 global financial crisis and its precursors, and the 2015 stock crashes in China. Moreover, a sharpest needle-like peak in relative entropy curves, especially for SSE market, always served as a precursor of an unusual market, a strong bull market or a bubble, thus possessing a certain ability of forewarning.