Most dinoflagellates have two flagella inserted into their cell wall via the flagellar pore(s) at approximately the same location. In most dinoflagellates one of the flagella wraps around the cell and is known as the transverse flagellum, while the other, longitudinal flagellum, extends tangentially to the cell, perpendicular to the plane of the transverse flagellum. The beating of the longitudinal flagellum and the transverse flagellum imparts a forward and spiralling swimming motion, and defines anterior (the direction of swimming) and posterior (opposite to anterior and the direction the longitudinal flagellum is directed). The flagellar pore and point of flagellar insertion defines ventral with the opposite side dorsal. Left and right sides of the cell are then defined as in most organisms. A depression often occurs on the ventral surface at the point of flagellar insertion, and is known as the sulcus. The transverse flagellum often occurs in a furrow known as the cingulum which encircles the cell except where interupted by the sulcus on the ventral surface.

The cell wall of dinoflagellates is subdivided into multiple polygonal amphiesmal vesicles of varying numbers (from half a dozen to hundreds). In some dinoflagellates, these vesicles are filled with relatively thick cellulose plates with bounding sutures. When this occurs, the cell wall is referred to as a theca. Dinoflagellates possessing a theca are often referred to as "armored dinoflagellates", while those without are referred to as "naked dinoflagellates".

Figure 1

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