The words fleas, flees sound the same but have different meanings and spellings. Why do fleas, flees sound the same even though they are completely different words?
The answer is simple: fleas, flees are homophones of the English language.
Plural form of flea.
To run away, as from trouble or danger: fled from the house into the night.
To pass swiftly away; vanish: "of time fleeing beneath him” ( William Faulkner).
To run away from: flee the scene of an accident.
Definitions from Wiktionary, Creative Commons Attribution/Share-Alike License, from The American Heritage® Dictionary of the English Language, 4th Edition and Wordnik.
Homophones (literally "same sound") are usually defined as words that share the same pronunciation, regardless of how they are spelled.
If they are spelled the same then they are also homographs (and homonyms); if they are spelled differently then they are also heterographs (literally "different writing").