The oncogenic virus from the Herpesviridae family is the causative agent of Marek's disease, which is characterized by the formation of lymphoid neoplastic changes, immunosuppression and transient paralysis in chickens. Marek's disease has a significant economic impact due to high mortality and morbidity, although it does not exhibit zoonotic potential. However, high losses, due to organoleptic changes, represent a major problem in the poultry industry. The Marek's disease virus is ubiquitous and spreads horizontally. Due to the increasing virulence of MDV, an effective strategy for control is needed. For control, immunoprophylaxis is used, with the vaccination using CVI988 strain as the golden standard. This vaccine provides protection against very virulent strains and is most commonly administered to day-old chicks. All vaccines could protect against mortality, clinical signs, and the frequency of lesion occurrence, but none provide complete protection from infection, replication, and shedding of the wild virus. For a better understanding of the mechanisms of vaccine protection, it is useful to monitor vaccine and wild strains of MDV. For this purpose, qPCR testing could be used on feather and dust samples. This study investigated the presence of vaccine and wild strains of MDV in feather and dust samples from two farms, on seven flocks in total. The CVI988 vaccine strain was in significantly higher percentage detected in chicken flocks up to three weeks, compared to older flocks, in which detection was absent. The wild MDV strain was present in a higher percentage in flocks at the start of production and of intermediate age, while it was not detected in chicks and older flocks. The exception was flock K3, where a higher prevalence of the vaccine strain was recorded. Results emphasise the importance of MDV strain monitoring with the aim of monitoring immunoprotection and spread and environmental contamination with wild strains.