Study of long-distance dispersal (LDD) theory requires a method for marking live LDD pollen. Such a method must complement the more intensive sampling methods involving molecular cytogenetics, proteomics, and genomics. We have developed a new method for marking live Pinus taeda pollen using two dyes, rhodamine 123 and aniline blue, dissolved in a sucrose solution. Marked and unmarked pollen were compared with respect to in vitro germination, storage, terminal velocity and in vivo pollen-tube penetration of ovules. We found that: (1) both types of marked pollen retained their capacity for germination, (2) both types of marked pollen had similar aerodynamic properties as unmarked pollen controls, (3) marked pollen retained its germination capacity for 48 h, and (4) of the marked pollen, only the aniline-marked pollen penetrated ovules during pollination. Germination declined rapidly for both types of marked pollen after 48 h and before 37 days at -20°C storage, while the unmarked pollen lots retained 93% germination at all stages. Our method for marking live P. taeda pollen is feasible for tracing LDD pollen if released and deposited within 48 h of dye treatment.