Botryllophilus millari is described on the basis of females living in the compound ascidian Eudistoma caeruleum (Sluiter, 1898) collected in Madagascar. The new copepod provides the diagnostic morphological characters for subgroup 2 of female morphotype A (urosome 5-segmented) of the genus, but armature formula (setae and spines) for right and left legs 1–4 is assigned to the new formula pattern III; seven congeners of subgroup 2 have formula pattern II. The new species is also characterized by the following morphological features including the unique features for legs 1–5: 1) body fusiform, segmentation of metasome indistinct; 2) first to fourth pairs of legs placed obliquely from left side toward right side; 3) right leg 1 exopod modified trapezoidal (medial margin elongated), with 6 long spines on oblique distal margin; and 4) leg 5 short stout, directed anterolaterally. The new copepod is the fourth and last species of Botryllophilus described from the Humes collection in Madagascar (1967).