Nitzschia navis-varingica is a diatom that is known to produce significant levels of amnesic shellfish poisoning (ASP) toxins. A total of 33 N. navis-varingica strains were isolated from four brackish water localities in the Philippines and Indonesia, and cultured to characterize the toxins produced. The isolates were analyzed for domoic acid (DA) and isodomoic acids A (IA) and B (IB) by HPLC with fluorescence detection. Two toxin composition types were detected that have not been previously described: strains producing only IB and strains producing DA–IA–IB. These two types were isolated from two different localities. Eighteen strains were isolated from the Philippines (northern Luzon Island). Among them, 10 isolates from Alaminos produced only IB with an average toxin content of 3.05 pg cell−1, seven isolates from Bulacan produced DA and IB with average toxin contents of 0.68 pg cell−1 and 1.18 pg cell−1, respectively. One isolate from Cavite produced DA, IA, and IB with a toxin content of 0.58, 0.20, and 0.92 pg cell−1, respectively. Fifteen isolates from Indonesia (Bone, South Sulawesi) produced only DA (four isolates) or DA with trace amounts of IB (eleven isolates), with an average toxin content of 2.38 pg cell−1 and 0.06 pg cell−1, respectively. Sub-strains were established from strains producing either of the three toxin types: IB, DA–IA–IB, and DA-trace IB. Results showed that the toxin composition type was the same for parent and sub-strains, indicating that the toxin composition is a stable character for a strain.