Vascular streak dieback (VSD) disease caused by Ceratobasidium theobromae is an important cocoa disease in Southeast Asia and Oceania. The symptoms originated in PNG by 1960s with a greening spot chlorotic sign and currently the expression is much more diverse, destructive and rampant while endophytic communities frequently associate with the symptoms. The study aimed to test the hypothesis that VSD symptom variation correlates with genetic diversity of C. theobromae. While this question remains unresolved I describe factors responsible for the diversity of VSD symptoms through a systematic hierarchical survey of cocoa farms across Sulawesi in different topographic altitudes to evidence pathogen interest on the tissue with a pair of specific primers Than_ ITS 1&2 and other fungi with ITS_1&4, then integrating in vitro, microscopic observation and PCR amplification. And, of 1,500 DNA samples from over 93 cocoa villages and 10 districts with various farmland characteristics, 65% of samples were positive sign for C. theobromae DNA. Other endophytic fungi frequently grew either before, or simultaneously, with the putative C. theobromae onto the media such as Ascomycetes Xylaria reevesiae (unreported species in Sulawesi), Lasiodiplodia theobromae, Fusarium and Colletotrichum species and therefore, co-infection hypothesis is proposed. By modified in vitro trial, basidiomata and protobasidia as generative structures formed like a globose and cylindrical hyphal apex which is important key in the identification Ceratobasidium and Thanatephorus species. A gradient of altitude contributes to cause symptom diversity. The lowest farmland often expressed the “old” symptoms in West Sulawesi while the “new” symptom was more often in highest lands of South and Southeast Sulawesi. No significant effect of temperature to variation occurs, but it exhibited the more humid farm, the more classical symptoms expression probably contributing to variations by helping fungal sporulation.