If it were πεπόνη, it would be a feminine noun, so it would be η πεπόνη. Feminine nouns tend to end in -η. Neuter nouns in -ι. So, it is good to remember the nouns with their article and try to memorize gender endings. If you find that being too much, you will just have to memorize it the way it is, unfortunately. There is no difference in pronounciation or something.
You can see noun endings here