Plant-specific fasciclin-like arabinogalactan proteins (FLAs) are a subclass of the arabinogalactan proteins (AGPs) superfamily. In addition to AGP-like glycosylated regions, FLAs have conserved fasciclin (FAS) domains. Here, we identified 220 FLA genes from seven Rosaceae species, including 38 FLA gene in pear. Based on gene structure and phylogenetic analysis, the Rosaceae FLA genes can be divided into four classes. The Ks and 4DTv values suggested that the PbrFLA gene family had undergone two whole-genome duplication events occurring at 30–45 MYA and ~ 140 MYA, respectively. Whole-genome duplication (WGD) and transposed duplication (TRD) events mainly drove the evolution of PbrFLA gene family. Most pear FLAs from pear had no intron in their genomic DNA sequences. Pear FLAs possess two highly conserved regions (H1 and H2) and the conserved [Tyr Phe] His ([Y/F]H) motif locating between these two regions. Based on gene expression analysis, most pear FLAs exhibited tissue-specific patterns. PbrFLA10, PbrFLA20, and PbrFLA21 were highly expressed in pollen tubes and self-pollinated styles, indicating FLAs play roles in pollen tube growth and self-incompatibility response. Repression of PbrFLA10/20/21 resulted in the acceleration of pear pollen tube growth. Taken together, our results provided information for understanding the evolution of the PbrFLA gene family and identified the key PbrFLAs genes regulating pollen tube growth.