A skeleton can be seen outside of Godzilla's underwater temple. This skeleton bears a body shape resembling Anguirus, a dinosaur who served as Godzilla's ally in a few films; the filmmakers have confirmed that it is in fact Anguirus.
One of the Titans, Leviathan, is in Loch Ness, implying that it's the origin of the Loch Ness Monster legend. Toho actually nearly made a kaiju film staring Nessie in 1978 in co-production with Hammer Horror and got far enough into production for posters to be made.
Mothra's eye-spots on her wings were designed to resemble Godzilla's eyes in order to create a connection between the two monsters. Michael Dougherty said 'she is his flag bearer and Queen.'
When asked if the "hollow Earth" civilization that prays at Godzilla's altar was new to the mythology, or was it an inversion of something he found going back to the Toho films, co-writer and director Michael Dougherty stated: "If you do go back and look at the entire library, there are sort of occasional references to lost civilizations. I mean, Mothra's followers are a perfect example, and so are Kong's followers. Mothra's egg tends to be housed in a mysterious temple surrounded by a singing and dancing troupe that's always trying to get her to hatch. So these creatures have a long history of being perceived as gods and deities. So it made sense to me that the Alpha of the group himself would also have a history, a deeper connection, to some ancient civilization that figured out how to spark and maintain a sort of symbiotic relationship with him, probably for their own protection. The same way that there are small fish that swim underneath a shark, or the tiny bird that pecks insects off elephants or rhinoceroses, human beings would be the tiny animals that seek protection under a much larger animal that simply puts up with their presence."
During a slideshow montage of all the numerous Titans that Monarch knows about, the scientific name shown for Kong is Megaprimatus Kong, which was his scientific name in supplementary material of King Kong (2005).