Papaya seedlings segregate for sex expression as females or hermaphrodites. Typically only hermaphrodite fruit are marketed in Hawaii. The agronomic practice of growing multiple seedlings that are later thinned to a single hermaphrodite tree is wasteful of seed, labor, and resources, especially when seed is costly. We compared growth of plants propagated by the clonal methods of micropropagation or rooting vegetative cuttings versus plants initiated as seedlings and transplanted. The seedlings were either single-planted hermaphrodites as identified by the polymerase chain reaction (PCR) or multiple-planted, thinned seedlings. The experiments were carried out in three different locations on two islands in Hawaii. Clonally propagated plants were significantly shorter than seedlings and bore flowers earlier and lower on the trunk at all locations. Stem diameter differences were not significant even though plant size was different at planting time. Percentage of trees in bud varied significantly in the third month after transplanting when about 90% of the rooted cuttings and large micropropagated plants had formed flower buds while only one multiple-planted seedling developed a bud. Overall, the clonally propagated plants were more vigorous and earlier bearing than were the seedling plants. There is good potential for adoption of clonal propagation when production becomes efficient enough to compete in price with the current practice of over planting and thinning.