A longitudinal section of the cell shows the anterior flagellar insertion and the positions of major organelles. Food vacuoles contain bacteria. The very short basal bodies, with transition regions recessed well interior to the plane of the cell membrane, are characteristic of Malawimonas and are not found in other similar flagellates.

The single mitochondrion is located next to, and mostly posterior to, the nucleus. The cristae are discoidal.

A single Golgi body/dictyosome lies next to the flagellar bases. This picture also shows some of the microtubular roots associated with the anterior end of the cell (see the drawing of the cytoskeleton, below).

The cytoskeleton is an asymmetrical system of two flagellar bases, three ventral microtubular roots, and a dorsal microtubular root from which secondary microtubules arise and fan out over the dorsal surface. Unlike other jakobids (Jakoba, Reclinomonas and Histiona), the left ventral root is not associated with a multilayered structure. Also, most of the microtubules that form the floor of the ventral groove come from the right ventral root; in other jakobids, these microtubules mostly come from the left root.

The posterior flagellum possesses a conspicuous and characteristic flagellar vane. The left picture shows its origin, near the anterior end of the cell. The right picture shows how the vane looks at approximately the middle of the cell. This vane arises on the ventral surface of the flagellum; in other jakobids, the vane arises on the dorsal surface. These pictures also show how the ventral microtubular roots appear in different parts of the cell (compare the map of the cytoskeleton, above).

The cyst is uninucleate, with one mitochondrion, and contains remnants of the kinetid (basal bodies and microtubular roots). It is surrounded by a thin wall, probably of organic material. The pad consists of fibrillar material, possibly representing adhesive polysaccharides. A pore in the wall in the vicinity of the pad may represent an exit aperture.

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