An incipient termite colony initially functions as a biparental family unit. The emergence of the first workers initiates the transition from biparental to alloparental care within a colony. During this transition, the number of protozoa harbored by Reticulitermes speratus (Kolbe) kings and queens is dynamic. In Coptotermes gestroi (Wasmann), the transition to alloparental care is completed by 150 days after colony foundation. In the present study, we quantified the protozoan abundance of C. gestroi and Coptotermes formosanus Shiraki kings and queens at ten time points during the transition from biparental to alloparental care (0–400 days post colony foundation). The protozoan abundance of C. gestroi and C. formosanus kings and queens peaked on either day 35 or 60 during the biparental care period, and then progressively decreased during the remainder of the study. By day 400 the protozoan abundance of kings and queens was either similar to or less than the abundance observed within unmated dealates. Both C. gestroi and C. formosanus kings and queens still harbored protozoa at day 150 even though the transition to alloparental care was completed by this time. On days 250 and 400 for C. formosanus, and on day 400 for C. gestroi, the protozoan abundance of kings was greater than the abundance of queens. These results indicate that alloparental care can become set within a colony prior to the loss of protozoa within the royal pair, and that queens lose their protozoa earlier than kings during incipient colony development.