The words gene, jean sound the same but have different meanings and spellings. Why do gene, jean sound the same even though they are completely different words?
The answer is simple: gene, jean are homophones of the English language.
A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism. Genes undergo mutation when their DNA sequence changes.
A heavy, strong, twilled cotton, used in making uniforms and work clothes.
Pants made of jean, denim, or another durable fabric.
Definitions 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").