The present study was undertaken to evaluate ectopic new bone formation effects of apatite-coated silk fibroin scaffolds (mSS) seeded with adenovirus-mediated bone morphogenic protein-2 gene (AdBMP-2) transduced canine bone marrow stromal cells (bMSCs) in nude mice. In this study, bMSCs derived from canine were cultured and transduced with AdBMP-2 adenovirus-mediated enhanced green fluorescent protein gene (AdEGFP) in vitro. Osteogenic differentiation of bMSCs was determined by alkaline phosphatase (ALP) activity analysis, and the transcript levels for BMP-2, osteopontin (OPN), osteocalcin (OCN) and bone sialoprotein (BSP) genes via real-time quantitative PCR (RT-qPCR) analysis. The ectopic bone formation effects of mSS seeded with AdBMP-2-modified bMSCs were evaluated through histological and histomorphological analysis 4, 8 and 12 weeks post-operation in nude mice. ALP activity was statistically increased in the AdBMP-2 group, when compared with control groups. The mRNA expression of BMP-2, OPN, OCN and BSP was also statistically up-regulated 6 and 9 days after AdBMP-2 transduction. Significantly higher bone volume was achieved in AdBMP-2-transduced bMSCs/mSS constructs than that of AdEGFP-transduced bMSCs/mSS or bMSCs/mSS groups at 4, 8 and 12 weeks (P < 0.01). These results demonstrated that mSS seeded with AdBMP-2-transduced canine bMSCs can promote ectopic new bone formation and maturation in nude mice, suggesting the potential of this silk-scaffold-based tissue-engineered bone for further bone regeneration studies in canine models.