Fifty morphological characteristics, fruit production over 3 years (from 1999 to 2002) and the amplified fragment length polymorphism (AFLP) technique were used to analyse a set of 48 guava (Psidium guajava L.) accessions cultivated in Mexico, in order to characterize their genetic relationships. Germplasm was collected from the Calvillo-Cañones region and planted in Huanusco, Mexico. The study included two P. cattleianum (Sabine) and two P. friedrichsthalianum (Berg-Niedenzu) accessions from Costa Rica as outgroups. Principal component analysis (PCA) explained less than 30% of total variation and 14 characteristics from trees (1), leaves (2) and fruits (11) were the most informative. PCA analysis separated the germplasm into three major groups of accessions based on fruit size and weight, stem diameter and leaf size. Significant differences in fruit yield were detected among accessions and years, where P. guajava produced 36 kg/year/tree of fresh fruit while P. cattleianum and P. friedrichsthalianum showed fruit yield lower than 7 kg/year/tree. The fruit yield broad sense heritability was 0.25. The AFLP analysis produced two clusters of Psidium accessions, the first included P. cattleianum and P. friedrichsthalianum, and the second P. guajava accessions. This is the first report about the use of AFLP marker methodology for the genetic characterization of Mexican native guava germplasm and the results based on phenotypic and productive characteristics suggest that germplasm was selected from open pollinated trees.