Population structure, activity patterns, habitat management, and the prevalence of upper respiratory tract disease were examined in two distinct populations of gopher tortoises (Gopherus polyphemus) on NAS Cecil Field, western Duval County, Florida. Surveys were conducted to evaluate differneces in population estimation. Significant differences were observed between observers; however, there was no difference in estimates obtained from line or strip surveys.A new technique for determining tortoise activity patterns was evaluated. Tortoises were found to be most active between 1000 and 1900 hours with peaks of activity between 1200 and 1700 hours. Success of the new technique was limited and future modifications are needed.Population structure at both sites was evaluated through the use of burrow width measurements. The Gate 11 site had significantly fewer juvenile burrows (4%) than did the OLF Whitehouse (39%). The subadult size class (140-230 mm burrow width) comprised the largest percentage of individuals for each site. Density estimates for the Gate 11 site and OLF Whitehouse were 3.3 tortoises/hectare and 7.1 tortoises/hectare, respectively. A total of 58 individuals were captured (both sites). Analysis of data both between and within sites did not reveal a sex ratio that was significantly different from 1:1. Mean carapace length did not differ significantly between males and females.A forest thinning operation was completed at the Gate 11 site. Fifteen percent (n=72) of the tortoise burrows were impacted by heavy equipment. Canopy cover was reduced from 80% to 30% and 3 months postharvest a 16% increase in burrow number was observed.Fifty individuals were sampled for the presence of upper respiratory tract disease. All ELISA positive (n=1) and suspect (n=3) tortoises were from the Gate 11 site. One positive was obtained from PCR analysis at the Gate 11 site; however, this was not M. agassizzi, but a previously unrecognized mycophasma.