Porphyra shares the same ultrastructural features of other red algae. The cells have a microfibrillar wall, although in the blade phase of Porphyra the fibrils consist of a xylomannan, whereas in the conchocelis they consist of cellulose as in other red algae. Mitochondrial cristae are flattened. Plastid thylakoids are never united into groups, and phycobilisomes appear on the external faces of the thylakoid membranes. Centrioles and basal bodies are entirely absent. The mitotic spindle, which is highly organized, is initiated in the vicinity of two ring-shaped spindle pole bodies.

The pit connections in conchocelis filaments feature a pit plug that consists of a proteinaceous core and a single outer cap. The cap is not separated from the core by a membrane. This pit plug configuration separates Porphyra and its relatives from all but two (the Hildenbrandiales and the Gelidiales) of the other groups of red algae that have pit connections.

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