Zygarde 50% Forme's appearance is based on a serpent in the shape of the letter Z. It may also draw inspiration from the sea serpent Jörmungandr and the dragon Níðhöggr. Jörmungandr is a child of Loki which surrounds the Earth; when he lets go, the world will end. Jörmungandr is a classic example of an ouroboros. Níðhöggr is a creature described as both a dragon and a serpent in the Prose Edda. Níðhöggr resides at the bottom of the world tree Yggdrasill and gnaws at its roots. It comes from the dark mountains of Niðafjöll and lives in Náströnd. The patterns spread across Zygarde 50% Forme's body are similar to ribose and deoxyribose molecules. Its tail's shape is possibly based on base pair codons, the essential building blocks of the DNA double helix.

Zygarde 10% Forme appears to be based on Fenrir, one of the children of Loki. The green scarf-like object around Zygarde 10% Forme's neck could be based on Gleipnir. Zygarde 10% Forme's razor sharp teeth may be an allusion to Fenrir biting off the right hand of Týr. This Forme could also draw inspiration from Garmr, the dog of Hel and watchdog that guards Helheim's gate. Zygarde 10% Forme's appearance resembles a Doberman Pinscher.

Zygarde Complete Forme is based off of Hel, the half-dead and half-alive ruler of Helheim in Nordic myth. Along with Jörmungandr and Fenrir, Hel is a child of Loki. A jötunn, known as Helreginn may have inspired Zygarde Complete Forme's gargantuan size, as it is believed by many scholars to be Hel herself. The uppermost section on Zygarde Complete Forme resembles a crown with jewels embedded within it, which may be a reference to Hel's title of Queen Hel in Bartholomeus saga postola. The colors on Complete Forme's chest match the colors of the real-world flag of France, the country which inspired the region of Kalos. The red and blue markings on either side of Zygarde Complete Forme may represent Yveltal and Xerneas, as this Forme exceeds both of their powers.

Zygarde Cell and Zygarde Core are based on both cells and flatworms, specifically planaria. Planaria and other similar flatworms are notable for their regenerative abilities, and will eventually form into multiple creatures if split apart. The fact that many Zygarde Cells make up a single larger creature may be in reference to this. Some planarians' ocelli also resemble eyes, which may have inspired the designs for the Cell and Core Zygarde. The hexagons within them likely represent a cell nucleus.