* Dreyfus Foundation Teacher- Scholar Award (1986)
* Alexander Von Humboldt Fellows Award (1990)
* Alexander Von Humboldt Award (1993)
* Elected, Fellow of the Meteoritical Society (1996)
* Ernest O. Lawrence Medal, Department of Energy (1998)
* Chancellors Associates Endowed Chair (1999–present)
* American Chemical Society (San Diego) Distinguished Scientist of the year (2002)
* Elected, Fellow, American Academy of Arts and Sciences (2002)
* Distinguished Alumni Award, Old Dominion University (2003)
* Press Club Headliner of the Year 2002 (2003)
* Selected, San Diego City Beat, 33 People to Watch in 2003 (2003)
* Creative Catalyst Award, UCSD-TV  (2003)
* Elected, Phi Beta Kappa (2005)
* Elected, National Academy of Sciences (2006)
* Minor Planet Named in his Honor: Asteroid (7004) Markthiemens. International   Astronomical Union (2006).
* Elected, Fellow American Geophysical Union (2006).
* Elected, Fellow, Geochemical Society (2007)
* Elected, Fellow, European Association for Geochemistry (2007)
* Graduate Made Good, Distinguished Alumni, Omega Delta Kappa Honor Society, Florida State University (2007)
*V.M. Goldschmidt Medal; The Geochemical Society. Awarded in Davos, Switzerland (2009)
* Selected one of 100 Distinguished Graduates in 100 years of Florida State University History (2010).
* Cozzarelli Prize, U.S. National Academy of Sciences for outstanding paper in Physical Sciences in the Proceedings of the National Academy of Sciences (2011).
* Elected Fellow, American Association Arts and Sciences (2013).
* Albert Einstein Professor, Chinese Academy of Sciences (2014).
* Leonard Medal of the Meteoritical Society (2017)
* Miller Visiting Professor, University California Berkeley (2017)
* Gauss Professorship, Göttingen Academy of Sciences, Germany (2017)
* Gauss Professorship, Göttingen Academy of Sciences, Germany (2020)