Protein kinase D (PKD), a member of the Ca²⁺/calmodulin-dependent kinase (CaMK) superfamily, is a serine/threonine kinase expressed as three isoforms (PKD1, 2, and 3). PKD has been suggested at the crossroads for the Bone Morphogenetic Protein-Insulin-like Growth Factor1 (BMP-IGF1) signaling axis, which plays a major role in bone formation. This article focuses on the roles of PKD1 and 2 in the mouse skeleton. Dual-energy X-ray absorptiometry (DEXA) scan analysis of male and female pubescent mice revealed a significantly decreased bone mineral density (BMD) in the whole body and femoral bone of mice with one inactive PKD allele PKD1 (+/-), compared to their wild-type littermates. The body weight, nasal-anal length, and percent body fat of the mice were not significantly different from their wild-type littermates. In PKD2 (+/-) male, but not female mice, significantly decreased BMD in the whole body, spine, and femoral bone was detected, compared to their wild-type littermates. Lower expression levels of osteoblast and osteoclast differentiation markers were detected in cultured bone marrow stromal cells (BMSC) from PKD1 (+/-) male mice compared to wild-type mice. In female mice, only markers of osteoblast differentiation were reduced. Cultured mouse calvarial cells from PKD1 (+/-) mice demonstrated substantially reduced BMP responsiveness and BMP type II receptor mRNA expression levels. Cultured BMSC from male PKD2 (+/-) mice exhibited lower mRNA expression levels of osteoblast differentiation markers and higher levels of osteoclast differentiation markers than wild-type. However, osteoblast and osteoclast differentiation markers were reduced in female PKD2 (+/-) mice. BMC cultures from male and female PKD2 (+/-) mice displayed a reduced BMP responsiveness without any significant changes in BMP receptor mRNA expression levels. These data suggest that PKD1 and 2 share common but also distinct mechanisms in the regulation of osteoblastogenesis and osteoclastogenesis that are manifested during mouse puberty in a gender-specific manner.