Forensic botany, the use of plants as evidence in criminal investigations, is a well-established forensic science discipline that itself comprises a number of specialties including, inter alia, plant anatomy, palynology (pollen analysis), and plant systematics. During the commission of outdoor crimes, plant material may be transferred from the crime scene to the victim or perpetrators.  This plant material may be probative due to the restricted geographical distribution of the plant species or individual genotype identified. Although the principal experimental tool of the forensic botanist remains the light microscope, intraspecies genetic variation is best determined by molecular genetics methods.  Pre-molecular genetic forensic botany has played a significant role in a number of criminal cases.  Analysis of wood evidence was utilized in the 1932 Charles Lindbergh baby kidnapping case.⁵³ In 1994, a grave containing 32 male skeletons was discovered in Germany, and analysis of pollen spores recovered from the nasal cavities of the skulls was performed. Based on types of pollen prevalent during different seasons, identification of the type of pollen allowed for identification of the group of men and determination of when they were killed.⁵⁴

Molecular genetics methods for detection of nucleotide sequence polymorphisms in plants include randomly amplified polymorphic DNA markers (RAPD), amplified fragment length polymorphisms (AFLP), and simple sequence repeats (SSR).^53-56 RAPD analysis uses random primers, around 10 nucleotides in length, which hybridize to multiple sequences throughout the genome. If two primers hybridize to opposite strands within close enough proximity to one another, they will amplify a region between the two primers. Since sequence variation exists between DNA from different sources (insertions, deletions, nucleotide polymorphisms), it is possible that the primers may not hybridize in the same locations and thus result in the recovery of a different number of amplification products. AFLP utilizes restriction enzymes (RE) to detect RFLP (Restriction Fragment Length Polymorphism) variation. After RE digestion, nucleotide adaptors are ligated to the restriction fragments and amplified using appropriate adaptor-specific primers.  The resulting multilocus RAPD or AFLP profiles may be sufficiently discriminatory to permit species identification or individualization.  However, many of these multilocus fingerprinting methods suffer from poor reproducibility and low sensitivity. Consequently single locus microsatellite techniques, akin to human STRs (Short Tandem Repeats), are increasingly being used.

The first reported application of plant DNA evidence involved the molecular identification of seed pods from a Palo Verde tree used to link a suspect to a particular crime scene (see example below).⁵⁷ RAPD analysis has been used in a lawsuit involving a suspected theft of an Italian patented variety of strawberry, "Marmolada." The RAPD amplification products of the suspected plants confirmed that the farmers had unlawfully grown the patented variety, and this evidence was accepted in court.⁵⁸

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