Truncal acne represents a biologically distinct manifestation of acne vulgaris, yet its fungal ecology remains incompletely characterized. Previous work using internal transcribed spacer 2 (ITS2) sequencing suggested that truncal acne is associated with altered fungal richness and Malassezia species composition; however, fungal marker choice may influence ecological inference, particularly in sebaceous skin dominated by Malassezia. In this study, we characterized the truncal skin mycobiome of patients with truncal acne and healthy controls using internal transcribed spacer 1 (ITS1) amplicon sequencing. Skin swabs were collected from the upper back, and fungal communities were analyzed using QIIME 2 with taxonomic assignment against the UNITE v10.0 database. Baseline acne–control differences and doxycycline-associated patterns were evaluated using alpha- and beta-diversity metrics and differential abundance analyses. Doxycycline-associated patterns were assessed using paired, within-patient pre- and post-exposure comparisons. ITS1 profiling demonstrated that truncal acne was associated with altered baseline fungal ecology compared with controls, characterized by reduced alpha diversity and ASV-level differences within Malassezia-dominated communities. Beta-diversity analyses showed substantial overlap between acne and control samples, indicating limited global separation. Following doxycycline exposure, fungal communities remained Malassezia-dominant and did not demonstrate uniform convergence toward control profiles; instead, species- and ASV-level differences were heterogeneous across individuals and exposure durations. Together with prior ITS2-based findings, these results underscore the importance of marker-dependent perspectives when interpreting fungal ecology in sebaceous skin.