Organization within Phycokey is based on separation of morphological features easily recognizable in a student-grade microscope. The first level of separation is generally the most apparent: unicells (single cells), colonies, and filaments.
Secondarily, where useful, unicells are separated on the basis of flagellated and non-flagellated, or symmetric and asymmetric (as in the diatoms). In other cases the extracellular presence or absence of a sheath is useful.
Filamentous forms are separated into branched and unbranched, tapered or untapered, cell differentiation or not, sheath present (filaments) or no sheath (trichomes), and similar attributes where useful.
Additional characteristics useful in various groups include chloroplast characteristics (shape and number per cell), spores, cell connections in colonies and filaments.
Conjugate greens (desmids and non-desmids) are separated from non-conjugate greens even though this is not directly and explicitly through their morphology.
In summary the navigation via morphology in Phycokey is similar to that used in many standard dichotomous (bifurcate) keys, but with the added advantage of comparing many more than just two images at any stage of decision making that leads to a genus.