Stem cells are cultured under non-physiological conditions. Placental trophoblast stem cells (TSC) are isolated from the embryo where fibroblast growth factor (FGF)4 and low, 2% O2 maintain pluripotency and proliferation. However, TSC are cultured with FGF4 and 20% O2 that causes TSC differentiation and suppresses proliferation. We test the hypotheses that stress-activated protein kinase/jun kinase (SAPK/JNK) in TSC (1) responds to contradictory culture signals (FGF4 and 20% O2), (2) reports optimal O2 levels for TSC culture, and (3) adapts TSC to relative roles of changing O2 and FGF4 levels. We found that SAPK is activated when TSC are cultured with FGF4 and 20% O2, but that SAPK decreases when FGF4 is removed and TSC remain at 20% O2, or when TSC are shifted from 20% to 2% O2 with FGF4. The two low SAPK activation states are not the product of a common biological effect as FGF4+2% O2 provide two pluripotency signal and 20% O2 (-)FGF4 provide two differentiation signals. Two lines of evidence suggest that FGF4 does not directly activate SAPK. One is the transient increase in pSAPK with FGF4 removal at 2% O2. The second is the loss of pSAPK with continuing FGF4 when O2 is switched from 20% to 2%. Thus, SAPK is activated when the contradictory signals are present, but is deactivated about 3-5fold when either of the contradictory signals is removed. Addressing the second hypothesis we found that 2% O2 induces highest TSC accumulation rates and lowest SAPK activation. In contrast 20% or 0% O2 activate 5-20-fold higher levels of SAPK and also leads to significantly lower TSC accumulation rates. Addressing the third hypothesis, at any O2 level the role of SAPK is to induce Hand1+ differentiated trophoblast giant cells and to suppress Gcm1+ positive alternate differentiated lineages. For TSC accumulation rates, at 2% there is a large, significant increase that is dependent on synergism between O2 and FGF4 signals, but not dependent on SAPK activity. For mitochondrial function (charge gradient) FGF4 is dominant in suppressing function at 2% or 20% O2 and function initiates when FGF4 is removed at 2% or 20%. We also study invasion/migration of TSC lineage cells and pluripotency of TSC and have observed effects of FGF4 and O2 that can be regulated by SAPK. Conclusions: We found that SAPK was activated when the contradictory signals were present and decreased when either contradictory signal was removed and that the lowest levels of activated stress enzyme (SAPK) reports the optimal culture conditions for stem cells. Significance. The findings are important in suggesting that stress enzymes sense suboptimal signals during stem cell culture and probably in vivo. SAPK mediates stress response functions such as lineage choice and suppression.