Ibrutinib and acalabrutinib are Bruton's tyrosine kinase inhibitors (BTKis) that are effective therapies for chronic lymphocytic leukemia (CLL). While clonal evolution during ibrutinib treatment has been investigated, the impact of clonal evolution during acalabrutinib treatment is unknown. We collected B-cell samples from 39 individuals receiving BTKi treatment annually for 3 years, with an additional sample taken at the most recent visit during the study period. Using this longitudinal data, we have reconstructed the clonal evolution of each patient using somatic mutations found within the B-cell populations. Three distinct patterns of clonal evolution were identified: 1. new clone emergence; 2. clonal selection; 3. clonal replacement. As previously seen in patients treated with ibrutinib, the evolution of subclones containing CLL-driver mutations is significantly associated with negative outcomes for patients treated with acalabrutinib (Log-rank p=0.04). Subclones containing C481S BTK mutations (a well-known resistance mechanism) developed in three patients from each BTKi cohort in a median of 3 years (range=2-3.5). Understanding the clonal evolution within patients treated with either of these BTKis can help determine how well a patient maintains response to treatment and if BTKi treatment should be modified or another agent should be added to deepen response.