Sandalwood spike disease (SSD) is a serious disease of Indian sandal tree (Santalum album). The disease is caused by a Candidatus Phytoplasma asteris strain of subgroup 16SrI-B. The disease is naturally spread through leafhopper and root-grafting. The infected plants take long time to express disease symptoms and eventually die. The diagnostic disease symptom of SSD is crowded small chlorotic leaves on stiff twigs that has spike like appearance. There are various biological, histopathological, electron microscopic and molecular methods available for the detection and identification of phytoplasma. Biological and histopathological tests are time consuming and ambiguous. Serological test like ELISA and molecular test like PCR are more versatile and accurate for the detection of phytoplasma. Application of various molecular techniques like nested PCR, RFLP and sequence analysis of 16S ribosomal RNA led to identify the SSD phytoplasma isolates as a member of 16SrI-B and 16SrXI-B phytoplasma subgroups. In this chapter, various diagnostic methods utilised for the detection and identification of SSD phytoplasma are summarised.