We use Fourier analysis to investigate evolutionary dynamics related to periodicities in marine fossil biodiversity. Coherent periodic fluctuation in both origination and extinction of “short-lived” genera (those that survive <45 Myr) is the source of an observed ∼62 million year periodicity (which we confirmed in an earlier paper and also found to be ubiquitous in global compilations of marine diversity). We also show that the evolutionary dynamics of “long-lived” genera (those that survive >45 Myr) do not participate in the periodic fluctuation in diversity and differ from those of “short-lived” genera. The difference between the evolutionary dynamics of long- and short-lived genera indicates that the periodic pattern is not simply an artifact of variation in quality of the geologic record. Also, the interplay of these two previously undifferentiated systems, together with the secular increase in abundance of “long-lived” genera, is probably the source of observed but heretofore unexplained differences in evolutionary dynamics between the Paleozoic and post-Paleozoic as reported by others. Testing for cycles similar to the 62-Myr cycle in fossil biodiversity superimposed on the long-term trends of the Phanerozoic as described in Paper I, we find a significant (but weaker) signal in sedimentary rock packages, particularly carbonates, which suggests a connection. The presence of a periodic pattern in evolutionary dynamics of the more vulnerable “short-lived” component of the marine fauna demonstrates that a long-term periodic fluctuation in environmental conditions capable of affecting evolution in the marine realm characterizes our planet's history. Coincidence in timing is more consistent with a common cause than with sampling bias. A previously identified set of mass extinctions preferentially occur during the declining phase of the 62-Myr periodicity, supporting the idea that the periodicity relates to variation in biotically important stresses. Further work should focus on finding links to physical phenomena that might reveal the causal system or systems.