The direct and therefore forgery-proof marking of singled horticultural products can be done by laser radiation. The potential codification and the harmless-ness of markings at micro scale were investigated. The use of different laser wave-lengths and parameter settings allows for superficial laser markings, which could be re-identified by image processing, and for sub-epidermal laser markings, which could be read by optical coherence tomography. Thus, parameter studies were performed using different laser systems (800 nm femtosecond-pulsed laser and a quasi-continuous wave 10,600 nm CO2 laser) on horticultural products (rhododendron cuttings and apples). An image processing algorithm was developed to evaluate the superficial laser markings. The sub-epidermal laser markings were re-identified using optical coherence tomography. Furthermore, the effect of the different laser irradiation (laser wavelength, applied laser energy, location of the marking) onto the product quality was determined concerning surface changes. Safe and re-identifiable laser markings could be labeled using wavelength-dependent energy doses. Sub-epidermal markings showed minor quality loss.