Summary *Ten axenic cultures, referred to as Fibrocapsa japonica, were studied for their morphology, pigment composition, toxicity and phylogeny. *Morphologically, all 10 accessions were similar and displayed equivalent pigment contents. We identified chlorophylls a and c, beta-carotene and fucoxanthin as the dominant pigments, together with xanthophyll cycle carotenoids likely to be involved in photoprotection. *All 10 accessions caused brine shrimp, Artemia salina, mortality and displayed haemolytic and haemaglutination activities toward sheep erythrocytes. Our results indicate that haemaglutination activity is a key component of F. japonica toxicity. *Examination of a collection of F. japonica expressed sequence tags (ESTs) has led to the identification of candidate genes involved in F. japonica toxicity and/or growth control.