Ponderosa pine is a widespread species with a great deal of geographic variation. Jeffrey pine has a much smaller geographic and ecological range than does ponderosa pine being confined to Baja California, California and the Siskiyou Mountains of Oregon.
There are a number of species of pine besides Jeffrey pine that are similar in appearance to ponderosa pine. One that springs immediately to mind is the Apache pine (Pinus englemanii) of the mountains of SE Arizona; another is the red pine of the lake states.
Based on chemical taxonomy, Jeffrey and ponderosa pine are clearly different species. And, the morphological differences between the two species, cone prickles, volatile terpine composition, foliage color and length of retention, are distinct.
Interestingly, if one looks at ponderosa pine across its range, there are some within-species morphological differences that are greater than those between Jeffrey and ponderosa. One striking difference is with pines growing in southern Arizona, SW New Mexico and west Texas. Here, ponderosa pines typically have five needles per bundle in contrast with three needles per bundle over the rest of the range. And, the five needle variety grows in mixture with the three needle variety in many places. Some taxonomists claim that the five needle variety of ponderosa pine (Pinus ponderosa [i]var Arizonica[/i] is a separate species from the three needle variety. I would personally like for it to be a separate species but, sadly, the science just doesn't back up the difference enough for the split.
May I walk in beauty.