The pair, surnamed Liao and Huang, will be charged with hunting an endangered animal after they allegedly killed the whale shark and sold its meat for around 2.5 yuan ($0.4) per kilogram.
Provincial Communist Party authorities also said the local fisheries chief would be investigated for “serious violation of discipline,” following the incident.
The case exploded online after two photos were uploaded showing the giant animal hanging from a crane, leading many to demand justice for the shark.
While Liao and Huang reportedly told police that the animal was dead and decomposing when they found it, many commenters online linked it to another shark spotted in the area, photos of which recently went viral.
Last week, oil rig workers in the area posted several photos of a whale shark they said was an “old friend,” who often came to visit the rig at this time of year.
The largest fish in the world, whale sharks are listed as “vulnerable” by the International Union for Conservation of Nature, just a step above endangered. They are deemed a second-class nationally-protected animal in China, and must be set free if caught.