Two new naturally occurring 1-aryl-2,3-naphthalide lignans, cilinaphthalide A (1) and cilinaphthalide B (2), and nine known compounds were isolated from the whole plant of Justicia ciliata. Their structures were established by spectral analysis, and their cytotoxic activity was evaluated against several different cell lines. The known compound, justicidin A, showed potent cytotoxic effects against T-24, CaSki, SiHa, HT-3, PLC/PRF/5, and 212 cells in vitro.