Small intestine neuroendocrine tumor (SI-NET), the most common cancer of the small bowel, often displays a curious multifocal phenotype with several intestinal tumors centered around a regional lymph node metastasis, yet the typical path of evolution of these lesions remains unclear. Here, we determined the complete genome sequences of 37 tumors from 5 patients with multifocal SI-NET, allowing elucidation of phylogenetic relationships between multiple intestinal tumors and metastases in individual patients. Notably, lack of shared somatic mutational events strongly supports that the intestinal tumors were of independent clonal origin. Furthermore, adjacent lymph node metastases arose from a single, typically centrally located, intestinal tumor. Thus, we propose that multifocal SI-NETs form primarily by independent somatic evolution rather than local metastatic spread.