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Parthenocarpy, the development of fruit without fertilization, is a significant trait in fingered citron (Citrus medica L. var. sarcodactylis Swingle). This study aims to elucidate the regulatory mechanisms underlying parthenocarpy through comparative transcriptome analysis and phytohormone profiling between fingered citron and its non-parthenocarpic counterpart, citron. A total of 66 differentially expressed hormone-related genes were identified, with the auxin pathway emerging as the most prominent in fingered citron. Protein–protein interaction analysis revealed a potential interaction between auxin and abscisic acid (ABA). Phytohormone content analysis indicated that fingered citron exhibited higher levels of indole-3-acetic acid (IAA) and lower levels of ABA compared to citron. A weighted gene co-expression network analysis (WGCNA) suggested that the interplay between auxin and ABA is crucial for triggering parthenocarpy. Virus-induced gene silencing (VIGS) experiments demonstrated that silencing CmsABI5 led to decreased ABA levels, while auxin levels remained unchanged, resulting in disrupted parthenocarpy and increased ethylene levels, indicating a secondary hormonal response. Additionally, gene expression changes associated with failed parthenocarpy showed down-regulation of SAUR50 and up-regulation of PP2C 56, linking these changes to ABA signaling. Our findings highlight the central regulatory role of auxin in parthenocarpy in fingered citron, with ABA acting as a critical modulator. The suppression of ABA alone disrupts parthenocarpy despite stable auxin levels, emphasizing the necessity of balanced hormone interactions. This research underscores the significant role of auxin, rather than gibberellin (GA), in regulating parthenocarpy in fingered citron, contributing valuable insights to the understanding of fruit development mechanisms. [ABSTRACT FROM AUTHOR]