The diseases huanglongbing [HLB, associated with Candidatus Liberibacter asiaticus (CLas)] and Asian citrus canker [ACC, caused by Xanthomonas citri (Xcc)] are widespread in Florida and many other citrus-growing areas, presenting unprecedented challenges for citrus breeding. Because HLB and ACC weaken trees and compromise cropping, breeding is much less efficient using seed parents that have been exposed to these diseases. Therefore, it would be highly desirable to use unique disease-exposed selections only as pollen parents with pollen applied to disease-free trees. However, there may be a risk of introducing these diseases using such pollen sources. To assess this potential, abundance of the pathogens associated with these diseases was assessed in anthers and flowers using quantitative polymerase chain reaction. Because CLas is systemic, levels on mature leaves from the flower source trees were assessed to see if the presence of CLas in flowers was associated with leaf levels. Disease-exposed trees were tested in 10 genotypes from each of three broad genotypic categories, which reflect different levels of susceptibility to the diseases associated with the pathogens studied: Poncirus trifoliata hybrids (most resistant to HLB), Citrus maxima and hybrids (susceptible to both diseases), and C. reticulata and hybrids (considerable resistance to ACC). Of the 30 samples of each tissue type analyzed for CLas, 88% of mature leaves, 69% of flowers, and 88% of anthers had one or more CLas bacterium per sample. The trifoliate genotypic group had significantly lower levels of CLas than the pummelo and mandarin groups in mature leaf samples, but CLas levels were more similar between groups in anther and flower samples, and the pathogen was present in most of the trifoliate hybrids tested. Mean numbers of CLas detected per nanogram nucleic acid were 100 to 800 times higher in mature leaf samples, most characteristic of HLB symptoms, compared with anther samples. Xcc DNA was detected in 30% of flower samples and 23% of anther samples. No significant differences in Xcc levels were found between tissue type or genotypic group. However, regressions between Xcc levels in flowers and percent of plant pedigree derived from mandarin had a negative correlation and an r2 of 0.159 (P = 0.029). The biology of CLas is consistent with the pathogen being present in anthers from unopened flowers, whereas the ACC pathogen detected inside flowers was likely the result of contamination despite great care in sample collection and handling. Where exceptional diligence to exclude HLB and ACC is appropriate, results suggest that there may be a risk of spreading these pathogens through use of pollen from trees on infected farms.