Material properties of living matter play an important role for biological function and development. Yet, quantification of material properties of internal organs in vivo, without causing physiological damage, remains challenging. Here, we present a non-invasive approach based on modified optical tweezers for quantifying sub-cellular material properties deep inside living zebrafish. Material properties of cells within the gut region of living zebrafish are quantified as deep as 150 μ into the biological tissue. The measurements demonstrate differential mechanical properties of the developing foregut organs progenitors: Gut progenitors are more elastic than any of the neighboring cell populations at the time when the developing organs undergo substantial displacements during morphogenesis. The higher elasticity of gut progenitors correlates with an increased cellular concentration of microtubules. The results infer a role of material properties during morphogenesis and the approach paves the way for quantitative material investigations in vivo of embryos, explants, or organoids.