Phytophagous insects are organisms that use any part of a plant as a food resource. Within this group, we focused on the pest insect Anastrepha obliqua, a fly that feeds on fruits of plants of different species and causes economic losses on the American continent. The ability of the larvae of this species to feed on various fruits (polyphagia) has been studied from different perspectives but never at the level of microRNAs. These interfering RNAs can regulate gene expression in tissues and organs of an organism. The objective of this work was to obtain the first micro-transcriptome and to determine its expression levels and possible target mRNAs when the third instar larvae of the species A. obliqua feed on fruits of plants of three different species: Spondias purpurea, Mangifera indica, and Averrhoa star fruit. A total of 116 microRNAs were identified in the study, of which 37 were completely new. 54 microRNAs were expressed in all larvae, regardless of the fruit, while 44 were detected in larvae that fed on a specific fruit. 21 microRNAs showed differential expression, and the annotation of the targets showed that these interfering RNAs have important genes that play roles in the development, feeding and detoxification of the larvae as possible targets. The construction of the first micro-transcriptome and the identification of possible targets for A. obliqua provide new information for understanding the mechanisms that control gene expression in this species of dipteran.