The English version of the theme song is interesting. For one thing, it is not a remixed version as the previous four movie themes were. This theme has the exact same music and tempo as the TV version. Another thing is that the composers did not create a second verse to the song "Master Quest," so it just has the same lyrics as the TV Version all the way through.

During the end credits, when Annie and Oakley are researching in the jail library, the find a book that has pictures of Lawrence III and his flying fortress from Pokémon the Movie 2000: The Power of One.

The town of Alta Mare is obviously inspired by Venice, Italy. The director took a trip there while in the planning stages of the movie and was inspired by it. Thus, waterways instead of concrete streets and Italian music throughout the movie.

Unlike the previous four movies, 4Kids did not create an original song for the end credits. Instead, they took a segment out of four of their older songs-"Pikachu's Good-Bye," "You & Me & Pokémon," "My Best Friends," and "Together, Forever"-and remixed them.

When the film was first announced in Japan, it seemed that one of the early story concepts was that Latios and Latias were going to be relatives of Lugia, and that Lugia was going to make a re-appearance. However, it was eventually scrapped.

The Japanese version is called "The Water Capitol's Protector Gods Latios and Latias." The English version is called "Pokémon Heroes: Latios and Latias."

In the original Japanese version, Latios and Latias were two children who washed up onshore on Altomare and were cared for by an old couple. One day, an evil rain came and threatened to destroy the town, but the children were revealed to be the legendary Pokémon and saved the town from the rain. In exchange, they gave the city the Soul Dew, and the Latios and Latias left. It had nothing to do with Kabutops or Aerodactyl.