Frustules are elongated, straight, and rectangular in girdle view. Valves are linear to slightly lanceolate. Valve margins are smooth, or with a slightly inflated middle portion and/or slightly inflated apices. In some taxa, one apex is rounded and the other tapers slightly. The sternum is well developed, occupying nearly the entire valve width and running nearly the entire length of the valve. The valve face curves abruptly into a steep, wide mantle.
The areolae are loculate and situated at the valve face/mantle junction. The foramina are internal with small circular openings that are deeply set into the valve surface them difficult to observe. Externally, either a single bar spans the opening of an areola or several Y-shaped bars occlude the opening. Additional silica struts or bars may reinforce the Y-shaped bars. At one end of the valve, the bars may be confluent forming a marginal ridge of varying length.
Protuberances or spines of varying morphology may be present at one, or both ends of the valve. A stout, sessile rimoportula is present at each apex and may be oriented parallel, oblique, or more rarely, perpendicular to the apical axis. Internally, the rimoportula is "double lipped”, with an outer and inner lip on either side of the process tube. The lips may be separated from each other or may appear as longitudinal lines bisecting each "lip". Its external opening is a simple large pore either at the valve face/mantle junction or beneath an apical spine or protuberance. In some cases, the external pore is recessed within a fissure. A smaller pore is typically present beneath the external opening of the rimoportula and the edge of the valve mantle, but may be lacking.
Species within the genus appear to be heteropolar, although the symmetry differences may be subtle. This heteropolarity may take several forms. It may be manifest as differently shaped valve apices (rounded vs tapering), protuberances/spines present at only one valve apex or of differing size in the same valve, and confluent areolar bars forming a marginal ridge at only one end of the valve.
The cingulum consists of two unperforated valvocopulae which are open at one end.
Two recently described species are worth mentioning here. Kato and Suto (2018) described Thalassionema bifurcum from Pliocene Subantarctic sediments. It exhibits the morphology typical for the genus, but the valve ends are distinctly bifurcate rather than rounded or tapered. The authors claimed that two rimoportulae were present at each valve apex, but the images show only a single rimoportula at each. Sugie and Suzuki (2015) described T. kuroshioensis from temperate Japanese coastal waters and wrote that unlike other species of the genus their new species was strictly isopolar. However, only 11 valves were examined in the holotype material.
Living cells contain numerous, small, discoid chloroplasts.
The cells form colonies which are either stellate, zigzag, or fan-shaped. Based on SEM observations of uncleaned material, Hasle (2001) found that attachment of adjacent cells is by triangular mucilage pads emanating from the apical part of the sternum and surrounding areolae. The external opening of the rimoportula and the small pore appears to be not involved in mucilage secretion.
Thalassionema is a small genus of mostly marine taxa. Many varieties of the generitype, T. nitzschioides, have been described, but further studies are needed to clarify their status (Hasle 2001).