Personally, we have found no difference. we have used both species and have been impressed with the results of using Carterii and Frereana. They have both exhibited superior anti-inflammatory and antidepressant qualities as well as have both worked wonders on respiratory and skin conditions. (And more, I'm sure)
With that said, we have not been able to find any (independent, peer reviewed) research showing a large difference between the two. For instance, look at this table showing the difference between the several different types of boswellia: http://www.hindawi.com/journals/ecam/2013/140509/tab3/
We have found several articles showing the benefits of each separate frankincense. Generally it looks like if a researcher is going to research Frankincense they will do their research on either one or the other (Carterii or Frereana).
They both are wonderful oils. We urge you to pray and seek the Holy Spirit's guidance when making choices for yourself or your family. We firmly believe they are both superior-quality Frankincense oils; if not, we would not carry them in our store.