We report on the application of off-axis electron holography and high-resolution TEM to study the crystal habits of magnetosomes and magnetic microstructure in two coccoid morphotypes of magnetotactic bacteria collected from a brackish lagoon at Itaipu, Brazil. Itaipu-1, the larger coccoid organism, contains two separated chains of unusually large magnetosomes; the magnetosome crystals have roughly square projections, lengths up to 250 nm and are slightly elongated along [111] (width/length ~ 0.9). Itaipu-3 magnetosome crystals have lengths up to 120 nm, greater elongation along [111] (width/length approximately 0.6), and prominent corner facets. The results show that Itaipu-1 and Itaipu-3 magnetosome crystal habits are related, differing only in the relative sizes of their crystal facets. In both cases, the crystals are aligned with their [111] elongation axes parallel to the chain direction. In Itaipu-1, but not Itaipu-3, crystallographic positioning perpendicular to [111] of successive crystals in the magnetosome chain appears to be under biological control. Whereas the large magnetosomes in Itaipu-1 are metastable, single-magnetic domains, magnetosomes in Itaipu-3 are permanent, single-magnetic domains, as in most magnetotactic bacteria.