In a word: genetics. Freckles, aka ephelides, often depend on your DNA — although sun exposure can cause them to first appear or darken. Freckles are different than hyperpigmentation, aka dark spots, in that they’re caused not by melanocytes (which produces your skin’s color) but the melanocortin-1-receptor — the major freckle gene, according to a study published in the 2001 issue of Human Molecular Genetics, conducted by doctors in the dermatology department at Leiden University in the Netherlands.