We demonstrate molecular control of nanoscale composition, alloying, and morphology (aspect ratio) in CdS-CdSe nanocrystal dots and rods by modulating the chemical reactivity of phosphine-chalcogenide precursors. Specific molecular precursors studied were sulfides and selenides of triphenylphosphite (TPP), diphenylpropylphosphine (DPP), tributylphosphine (TBP), trioctylphosphine (TOP), and hexaethylphosphorustriamide (HPT). Computational (DFT), NMR ((31)P and (77)Se), and high-temperature crossover studies unambiguously confirm a chemical bonding interaction between phosphorus and chalcogen atoms in all precursors. Phosphine−chalcogenide precursor reactivity increases in the order: HPTE < TOPE < TBPE < DPPE <TPPE (E = S < Se). For a given phosphine, the selenide is always more reactive than the sulfide. CdS(1-x)Se(x) quantum dots were synthesized via single injection of a R(3)PS-R(3)PSe mixture to cadmium oleate at 250 °C. X-ray diffraction (XRD), transmission electron microscopy (TEM), and UV/Vis and PL optical spectroscopy reveal that relative R(3)PS and R(3)PSe reactivity dictates CdS(1-x)Se(x) dot chalcogen content and the extent of radial alloying (alloys vs core/shells). CdS, CdSe, and CdS(1-x)Se(x) quantum rods were synthesized by injection of a single R(3)PE (E = S or Se) precursor or a R(3)PS-R(3)PSe mixture to cadmium-phosphonate at 320 or 250 °C. XRD and TEM reveal that the length-to-diameter aspect ratio of CdS and CdSe nanorods is inversely proportional to R(3)PE precursor reactivity. Purposely matching or mismatching R(3)PS-R(3)PSe precursor reactivity leads to CdS(1-x)Se(x) nanorods without or with axial composition gradients, respectively. We expect these observations will lead to scalable and highly predictable "bottom-up" programmed syntheses of finely heterostructured nanomaterials with well-defined architectures and properties that are tailored for precise applications [corrected].