The Tomtor massif of Paleozoic ultramafic alkaline rocks and carbonatites is located in the northern part of the Sakha Republic (Yakutia). The massif (its total area is ~ 250 km2) is ~20 km in diameter, with a rounded shape and a concentrically zoned structure. The core of the massif consists of carbonatites surrounded by a discontinuous ring of ultramafic rocks and foidolites. The outer part is composed of alkali and nepheline syenites. All rocks are weathered and covered with eluvium, which is the thickest after carbonatites enriched in phosphates and REE. The weathering profile consists of four layers, from the top: kaolinite–crandallite, siderite, goethite, and francolite. The highest-grade ores are observed in the bedded deposit which fills depressions in “sagging” eluvium. The ores are laminated and cryptogranular, with high Nb, Y, Sc, and REE contents (on average, 4.5% Nb2O5, 7–10% REE2O3, 0.75% Y2O3, and 0.06% Sc2O3). The highest-grade ores are natural Nb and REE concentrates. The total REE content in some layers is > 10%. The morphologic features of the highest-grade phosphate ores from the northern part of the Burannyi site were studied. The ore-forming minerals belong to the pyrochlore group, crandallite group (goyazite), and monazite-Ce. The pyrochlore group minerals occur mainly as crystals that were completely replaced by barium–strontium pyrochlore and/or plumbopyrochlore but retained the original faces; also, they occur as numerous conchoidal fragments. The grains of the pyrochlore group minerals sometimes have a zonal structure, with an unaltered pyrochlore core and a reaction rim. Goyazite occurs predominantly as colloform grains. According to SEM and TEM data, monazite occurs in the ores as ~50 nm particles, which cover the outer part of halloysite tubes (800–3000 nm long and 300 nm in diameter) as a dense layer and make up peculiar biomorphic aggregates. The mineralogical data, the occurrence of biomorphic aggregates, and the close association of organic remains with ore minerals suggest that the high-grade ores of the Tomtor deposit, including the Burannyi site, resulted from a hydrothermal–sedimentary process with a presumably important role of bioaccumulation of REE phosphates.