Dual-structure clock tree synthesis (CTS) is described. Some embodiments can construct a set of upper-level clock trees, wherein each leaf of each upper-level clock tree is a root of a lower-level clock tree. Each upper-level clock tree can be optimized to reduce an impact of on-chip-variation and/or cross-corner variation on clock skew. Next, for each leaf of each upper-level clock tree, the embodiments can construct a lower-level clock tree to distribute a clock signal from the leaf of the upper-level clock tree to a set of clock sinks. The lower-level clock tree can be optimized to reduce latency, power consumption, and/or area.