The Early Cenozoic alkaline complex of Morro de São João intrudes the Precambrian basement at the eastern end of the Rio de Janeiro coastline. It is mostly made up of melanocratic nepheline syenites and nepheline syenites, with subordinate clinopyroxenites, shonkinites (melasyenites), and alkali gabbros. Melanocratic nepheline syenites and nepheline syenites are cross-cut by thin dykes, ranging in composition from phonotephrite to phonolite. The mafic-ultramafic rocks are meso- to orthocumulates, with mineral compositions and whole-rock chemistry suggesting crystallization from a moderately evolved batch of magmas (potassic tephrite/phonotephrite). Melanocratic nepheline syenites and nepheline syenites likely represent magma-crystal mixtures, whereas a few fine-grained rocks roughly approximate liquid compositions; alkali syenites are typical cumulitic rocks. Major and trace element compositions reflect a genesis of clinopyroxenitic to shonkinitic rocks from tephritic parental magmas, which evolved toward phonotephritic and phonolitic compositions. Initial 87Sr/86Sr and 143Nd/144Nd ratios (0.7048-0.7061 and 0.51231-0.51239, respectively) overlap the values in the analog intrusions of the Serra do Mar province, supporting a genesis from similar parental magmas and source mantle. The dominant lithospheric components of the latter may be responsible for the potassic affinity and strongly incompatible element enrichment of the derived melts.