Rising atmospheric carbon dioxide may affect plant populations in the short term through effects on photosynthesis and carbon allocation, and over the long term as an agent of natural selection. To test for heritable effects of elevated CO2 on stomatal responses and plant fecundity in Raphanus raphanistrum, we grew plants from 12 paternal families in outdoor open-top chambers at ambient (35 Pa) or elevated (67 Pa) CO2. Contrary to results from a previous study of this species, total flower and fruit production were marginally lower under elevated CO2. Across families, stomatal index and guard cell length showed little response to CO2 enrichment, but these characters varied significantly among paternal families in both the direction and magnitude of their response to changing CO2. Although these family-by-CO2 interactions suggest that natural selection might affect stomatal characters when ambient CO2 levels increase, we found no significant correlation between either character and flower or fruit production. Therefore, our data suggest that while heritable variation for stomatal index and guard cell length exists in this population, selection due to increasing CO2 is not likely to act on these traits because they had no detectable effect on lifetime fecundity.