Product marking in horticulture aims at providing robust and permanent means of marking products and preventing theft, tampering and cheating by customers. Direct part marking has sought to provide solutions to these problems. However, unlike in industry where it has been successful, in horticulture there are still a lot of challenges that prevent successful marking and reading of directly marked barcodes on horticultural products. The laser energy, barcode size, product color and days of storage are important factors that affect the marking, quality and readability of directly marked Data Matrix (DM) on apples. Therefore, the objective of this study was to solve the aforementioned problems with these factors by using Synrad 48-5 CO2 laser (10,600 nm), to mark some apples using low energy levels. Laser energy, the skin of the product and the inertia of the laser beam affected the printing of the DM on the apples. Incomplete marking of the DM at some of the energies used resulted in the DM not being decoded. Generally, there was successful decoding on Golden Delicious compared to Kanzi and Red Jonaprince for 10 days of storage. On the average, the smaller barcode size produced a better detection of the code than the bigger size. The better detection on Golden Delicious can be attributed to the better contrast between the DM and its color. As the days of storage increased, detection decreased for Kanzi and Red Jonaprince. There is a future prospect for directly reading marked apples in real production systems.