Atypical Spitzoid lesions pose a distinct challenge in classification as they may comprise a mixture of both classic benign nevus and cutaneous melanoma characteristics. Immunostaining and molecular analysis, such as comparative genomic hybridization, can assist in narrowing the differential diagnosis. We present a case of a 5-year-old male with an atypical Spitzoid lesion on his back. Initial histopathology revealed a relatively symmetric lesion with mitotic figures and poor maturation of melanocytes with descent into the dermis. Immunohistochemistry demonstrated a loss of p16, and array comparative genomic hybridization revealed a loss of chromosome 9, supporting a diagnosis of invasive melanoma arising in conjunction with a remnant of a conventional melanocytic nevus. This case is the first in Canada to demonstrate the use of array comparative genomic hybridization for diagnosing melanoma in a young paediatric patient.