The Eocene-Oligocene Conejos and Oligocene-Miocene Hinsdale Formations consist of lava flows and volcanic deposits in southern Colorado and northern New Mexico. The Conejos Formation is a series of intermediate-composition lava, breccias and volcanoclastic deposits from subduction-related magmatism, whereas the Hinsdale Formation consists of bimodal mafic and silicic lava flows associated with rift-related magmatism. These formations present an excellent opportunity to evaluate the evolution of the magmatic system beneath the San Juan Mountains following the Oligocene ash-flow eruptions of the San Juan volcanic field and afterwards with the transition to rift-related magmatism from the initiation of the Rio Grande Rift. New zircon dates from two Conejos samples and one Hinsdale sample from U-Pb LA-ICP-MC differentiate the two formations. Ten zircon grains from one Conejos sample yielded a 206Pb/238U weighted mean age of 33.22 ± 0.24 Ma (2s, n=18) a with an MWSD=0.35 (18AG-16) and another sample yielded an age of 33.01 ± 0.18 Ma (2s, n=31) from 13 zircons with an MWSD= 0.52 (18AG-17). Nineteen zircons from one Hinsdale sample yielded a weighted mean 206Pb/238U age of 22.22 ± 0.043 Ma (2s, n=28) with an MWSD=0.97, which is consistent with previously reported ages. However, ages from the Hinsdale sample range from 21.5 to 23.4 Ma, suggesting there may be multiple magmatic sources or components in order to explain the variety of ages from a single sample. These U-Pb ages provide a dataset with an alternative method of dating the Conejos and Hinsdale Formations, which had been dated using K-Ar analysis. They also add to the sparse geochronologic data and better define the timing of the initiation of the Rio Grande Rift. Whole rock major and trace elements are used to characterize these two formations and to track the evolution of the transitional magmatic system. The Conejos rocks have higher abundances of the incompatible LILE, HFSE and HREE, whereas the Hinsdale rocks have higher abundances of the compatible elements and LREE. This is shown in different mineral fractionation trends and supports varying degrees of crustal contamination and different primary magmatic compositions. The magmatic processes that formed the Conejos and Hinsdale Formations changed during the evolution of the San Juan Mountains. Partial melting from the source of the Conejos Formation is shown by decreasing abundance of Rb with increasing silica. Fractional crystallization of the Hinsdale Formation is shown by increasing abundances of Rb with increasing silica and curvilinear trends of the major oxides. REE abundances show the origin of the primary magmas of the Conejos and Hinsdale Formations. Constant La and Yb with increasing silica in the Conejos rocks suggest a non-enriched mantle source, while higher abundances of Nb relative to Th/U and increasing La relative to Yb suggest OIB-source enriched-mantle in the Hinsdale. Ranges of Ba/Sr, Th/Nb and higher abundances of Yb relative to La with increasing silica suggest magma mixing occurred within the Conejos field. Additional Hinsdale mineral composition of biotite, feldspars, olivines and pyroxenes, and zircon morphology can be used to further identify rift-related rocks. Biotite grains contain more Mg than Fe; feldspars grains become very slightly both more calcic and more sodic, while the potassium decreases (potassium feldspar becomes more celsian and less orthoclase) toward the rim; olivines grains contain more Mg than Fe and are predominantly forsterite; pyroxenes grain contain more Mg than Fe. Different U/Pb ages and identification of different geochemical signatures of primary magmatic compositions provide insight into how the magmatic system beneath the San Juan Mountain evolved after initiation of the Rio Grande Rift. The Miocene Hinsdale Formation formed from rift-related magmatism by the inception of the Rio Grande Rift following subduction-related magmatism of the Conejos Formation.