In the previous studies of Calea in Bahia, some specimens were treated as C. candolleana but their morphology was called “particularly distinct”. Detailed studies on the currently accepted species and these specimens demonstrated that they represent two new species. Calea flagelliformis resembles C. candolleana, but differs from the latter by the villous (vs. pubescent to hispid) indumentum of stems, leaves and peduncles, and sessile (vs. petiolate, 1.5–4 mm) leaves. Calea nakajimae differs from C. candolleana by the lanceolate or ovate (vs. elliptic) leaf limb, and pappus scales 0.5–1.2 mm long (vs. 0.2–0.3 mm long). These new species are described, illustrated, mapped, and their conservation status and taxonomic affinities are discussed.