Isozyme analysis was the basis for determining the frequency of occurrence and the characteristics of zygotic plants in Swingle citrumelo seedling populations from various sources of open-pollinated seeds, in a commercial nursery of Swingle citrumelo before and after roguing, and in commercial orchards and rootstock trials where this rootstock was used. Most zygotic seedlings identified by isozyme analysis could be distinguished by careful examination of morphological characteristics. Frequencies of zygotic seedlings varied among seedling populations, but were in the range (≈5% to 10%) found in previous studies. Roguing based primarily on size and growth habit of seedlings was effective in removing some, but not all, zygotic seedlings. Most of the remaining zygotic plants in the rogued population were found among the smaller seedlings. Trees budded on zygotic rootstock seedlings were found in two of the three groves studied, and in some instances an apparent incompatibility was developing in young trees.