Gomphonema stoermeri has a more narrow axial area formed by the longer, more dense striae. Gomphonema caperatum is very similar, so much so that the two taxa may not be distinguished in the light microscope. The species are discernible in SEM, as G. caperatum has surficial wrinkles along the entire valve face, whereas G. insularum has a few centrally located shallow, rounded depressions. To date, the distribution of these taxa differ, with G. insularum known from the Hawaiian Islands, and G. caperatum found in continental North America.
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