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Physically Limnofregata looked similar to modern frigatebirds, but had shorter legs and wings. They stood 30 to 40 centimetres (12 to 16 in) tall when on the ground and had a wingspan of about 100 to 120 centimetres (3 to 4 ft). The beak was shorter than that of modern frigatebirds, and lacked the typical hook at the end, resembling a strong booby beak more than that of today's frigatebirds. The species differ conspicuously in size, with L. hasegawai being as much larger when compared to L. azygosternon as today's largest species of frigatebird (Fregata minor) is compared to the smallest extant one (Fregata ariel). The bill of L. hasegawai was notably larger still than that of its congener, whereas its feet were smaller, echoing a pattern found in the extant Fregata species.

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