Population-based series analyzing clinical implications of nodal versus extranodal presentation of marginal zone lymphoma (MZL) are lacking. We studied clinical differences and trends in incidence, therapy and survival of nodal and extranodal MZL, and of MZL at different extranodal sites, in a population-based cohort. All patients with localized (Ann Arbor stage I and II) nodal (n = 211), splenic (n = 54) and extranodal (n = 1449) MZL, diagnosed between 1994 and 2010, were selected from The Netherlands Cancer Registry. Between 1994 and 2010 the incidence of nodal and extranodal MZL increased. The incidence of gastric MZL decreased. Patients with nodal MZL received more chemotherapy and targeted therapies than their extranodal counterparts. A trend in time toward less chemotherapy and more irradiation was observed. Overall survival (OS) curves for nodal and extranodal MZL overlapped (5-year OS 76% and 77%, respectively). Patients with a primary gastrointestinal (GI) localization had inferior OS compared to patients with non-GI extranodal MZL (5-year OS 71% and 85%, p < 0.0001). Patients with localized extranodal MZL presented more commonly with stage I disease, but their clinical presentation and survival were otherwise similar to patients with localized nodal MZL. MZL arising in the GI tract does not have a good prognosis and requires a different treatment approach.