A study was conducted to analyze the endophytic assemblage in the velamen roots of Rhynchostylis retusa in two geographical regions of Kerala. The study aimed to assess the influence of geographical and seasonal factors on the fungal communities. 264 fungal isolates were identified and categorized into 11 distinct morphotypes based on culture morphology. Ascomycotina was the dominant group, accounting for 97.34% of the isolates. Lasiodiplodia theobromae emerged as the predominant species, regardless of location or season. The colonization frequency of the isolates was highest during the monsoon season and lowest during the pre-monsoon season. The rates of isolation and colonization, along with the Shannon diversity index, were found to be significantly dependent on the sampling site and season. The study highlights the importance of geographical and seasonal factors in shaping these fungal communities