Roosters are a traditional symbol of Shintoism, associated with the sun goddess Amaterasu. Shinto is a philosophy indigenous to Japan, and therefore thematically related to loyalty & nationality, like Mugen.
Jin's main fish is colored like a koi, the Japanese word for "carp". Koi are obviously symbols of Japanese culture, associated with love & friendship. Aquatic life is from the ocean, the realm of the storm god Susanoo, Amaterasu's sibling & counterpart.
Check out the story of Amaterasu & Susanoo, as it has obvious parallels to Mugen & Jin's relationship. Interestingly enough, they have a third sibling, Tsukuyomi, the god of the moon, who acted as a foil, kind of like Fuu. And Tsukuyomi's falling out with Amaterasu resulted from a conflict with the goddess of food... "Her stomach is like a cosmos unto itself!"