Polyploidy affects photosynthesis by causing changes in morphology, anatomy and biochemistry. However, in newly developed polyploids, the genome may be unstable. In this study, diploid (2×) and synthetic autotetraploids in initial (4×-C0) and 11th generations (4×-C11) of Phlox drummondii Hook were used to study the effects of chromosome doubling and genome stabilisation on leaf photosynthesis and anatomical properties. The light-saturated photosynthetic rate on a leaf area basis at 360 µmol CO2 mol-1 air (A360) was highest in 4×-C11 leaves, intermediate in 4×-C0 leaves, and lowest in 2× leaves. Rubisco amounts, CO2-saturated photosynthetic rate at 1200 µmol CO2 mol-1 air at PPFD of 1000 µmol m-2 s-1 (A1200, representing the capacity for RuBP regeneration), cumulative surface areas of chloroplasts facing intercellular spaces (Sc), all expressed on a leaf area basis, were all higher in 4× leaves than in 2× leaves, and stomatal conductance (gs) at 360 µmol CO2 mol-1 air was only higher in the 4×-C11 leaves. A360 for the 4×-C11 leaves was greater than that in the 4×-C0 leaves despite having similar amounts of Rubisco. This was presumably associated with a greater RuBP regeneration capacity, as well as an increase in Sc and gs, which would increase the CO2 concentration of Rubisco. These results indicate that the higher rate of photosynthesis in 4×-C11 leaves was not an immediate outcome of chromosome doubling; rather, it was due to adjustment and adaptation during the process of genome stabilisation.