The Central American rain forest endemic Annonaceae species, Annona pittieri and Cymbonopetallum costaricense, were studied looking for molecules with bioactive potential. The acetogenin Squamocin (1) isolated from A. pittieri showed cytotoxic activity against human acute lymphocytic leukaemia with a good selectivity against healthy blood cells. Additionally, from A. pittieri nine molecules were isolated, including a new 2-azaanthraquinone alkaloid, 4-methoxybenzo[g]isoquinoline-5,10-dione (2). From C. costaricense three molecules were isolated including a new 1-azaanthraquinone alkaloid, 6-hydroxy-9-methoxy-cleistopholine (3).