Abstract: Frequency synthesis is based on phase synchronizing PLL output across REFERENCE and VCO clock domains (including outputs for multiple PLLs), based on an input (REF-Domain) SYNC signal (phase timing reference). A frequency synthesizer includes a VCO to generate VCO_clk and a PLL output circuit, such as a channel divider, to generate PLL_OUT based on VCO_clk (in the VCO-Domain). The VCO loop includes a PD to phase compare an input PD_clock based on REF_CLK, and a VCO feedback signal based on divided VCO_clk (NDIV_out). SYNC alignment circuitry generates a SYNC alignment signal based on SYNC, PD_clk, and NDIV_out (REF-Domain), which is used to synchronize the PLL output circuit and PLL_OUT to SYNC. If a reference divider generates PD_clk, the SYNC alignment circuitry generates a reset to SYNC-align the reference divider. If the VCO loop uses fractional divide, the SYNC alignment circuitry resets the fractional modulator to a known sequence.