Unlike roots of most plant species, the primary root of cardón Pachycereus pringlei, a Sonoran Desert Cactaceae, exhibits determinate growth. The root apical meristem of seedling primary root exhausts and all cells in the root tip differentiate. Determinate growth of primary and most lateral roots results in the formation of a compact root system that provides seedlings an advantage for survival in a desert environment. In order to identify and characterize genes involved in root meristem maintenance and determinate root growth in P.pringlei, we employed mRNA-seq using IGA II. The 85 nt reads were assembled de novo into about 31,000 contigs using the CLC Genomics Workbench. The largest contig of 15,606 nt represented the longest plant transcript from the BIG gene. The transcriptome contigs were annotated using the similarity search against GenBank Ref-seq proteins. Differential gene expression was estimated in the primary root tip. Over 400 and almost 900 transcripts were up-regulated more than 5 times during initial and terminal phases of root growth, respectively. Sixteen putative transcription regulators were up-regulated during the initial phase. Significant conservation between P.pringlei and Arabidopsis was revealed for the amino acid sequences and RNA expression patterns for various genes. We also detected differences in expression profiles of some PIN auxin efflux carriers between P.pringlei and Arabidopsis mutants with determinate primary root growth. The cytokinin synthesis related genes are expressed during P. pringlei terminal phase of root development, suggesting that the root tip is functionally active after meristem exhaustion.