Lunares literally translates to "moles" or "beauty marks". It's a wonderfully specific and intimate word that you don't often hear in a love song, making it very memorable.
In one of the song's most famous lines, Shakira sings, "Yo puedo escalar los Andes sólo por ir a contar tus lunares" (I can climb the Andes just to go count your moles). This grand, romantic exaggeration (hyperbole) shows a deep level of intimacy and affection, suggesting that even the tiniest details of her lover are worth an epic journey.
This song is a huge declaration of love, built around the idea of luck. Shakira feels lucky for everything that brought her and her lover together, even the distance between them. She sings, "Suerte que en el sur hayas nacido" (Lucky that you were born in the south), suggesting their love crosses borders. She's so devoted she'd do anything, even "escalar los Andes sólo / Por ir a contar tus lunares" (climb the Andes just / to go count your moles). The song is full of these grand romantic gestures mixed with funny, very specific details. My favorite is when she says she's lucky her breasts are small so he won't confuse them with mountains!
The whole point comes together in the chorus, where she repeats that she wants to spend her entire life with this person: "Contigo, mi vida, quiero vivir la vida" (With you, my love, I want to live life). It's a passionate and slightly obsessive song about finding the one person who makes everything, from geography to your own body, feel like a stroke of good fortune.