McMenamin was born in Oregon, earned his B.S. at Stanford University in 1979 and his PhD at the University of California, Santa Barbara in 1984. In 1980, while at Santa Barbara he met his future wife, Dianna, also a paleontology graduate student, with whom he would co-author several publications. He joined the staff at Mount Holyoke College in 1984.
In 1995 McMenamin led a field expedition to Sonora, Mexico, that discovered fossils (585 million years old) which McMenamin argued belonged to a diverse community of early animals and Ediacaran biota. The paper was published in the Proceedings of the National Academy of Sciences of the United States of America where it was reviewed by Ediacaran expert James G. Gehling. In 2011, McMenamin reported the discovery of the oldest known adult animal fossils, Proterozoic chitons from the Clemente Formation, northwestern Sonora, Mexico. This discovery has not yet been published in a scientific journal following peer review. These fossils McMenamin argued were associated with the earliest animal trace fossils, the first known arthropod tracks, and the earliest evidence in the fossil record for a predation event. The latter interpretation has not been widely accepted by other paleontologists. Further up in this same stratigraphic sequence, McMenamin also discovered and named the early shelly fossil Sinotubulites cienegensis, a fossil that allowed the first confident Proterozoic biostratigraphic correlation between Asia and the Americas. In Lower Cambrian strata higher in the stratigraphic sequence, McMenamin also discovered important stem group brachiopods belonging to the genus Mickwitzia. During a Mount Holyoke College field trip to Death Valley, California, McMenamin and his co-authors found evidence indicating that the Proterozoic shelly fossil Qinella survived the Proterozoic-Cambrian boundary.
In 2012 McMenamin proposed that the enigmatic Cambrian trace fossil Paleodictyon was the nest of an unknown animal, a hypothesis which, if supported, may be the earliest fossil evidence of parental behavior, surpassing previous findings by 200 million years.
In an attempt to explain the unprecedented and rapid spread of vegetation over dry land surfaces during the middle Paleozoic, Mark and Dianna McMenamin proposed the Hypersea Theory. Their Hypersea is a geophysiological entity consisting of eukaryotic organisms on land and their symbionts. By means of a process known as hypermarine upwelling, the expansion of Hypersea led to a dramatic increase in global species diversity and a one hundred-fold increase in global biomass.
Mark McMenamin has repeatedly criticized conventional Neodarwinian theory as inadequate to the task of explaining the evolutionary process. Joining with Lynn Margulis and the Russian symbiogeneticists, McMenamin has emphasized the importance of symbiogenesis theory as one means of addressing the gap in our understanding of macroevolutionary change in conventional Neodarwinian terms. In his 1998 book "The Garden of Ediacara: Discovering the First Complex Life", McMenamin argued that a Teilhardian rather than Neodarwinian approach is far better for trying to understand the evolution of the enigmatic Ediacara biota. In subsequent work, McMenamin emphasized the strength of the Teilhardian approach in comparison to alternate views and has highlighted what he calls the collapse of Neodarwinian theory. McMenamin argues that Neodarwinian gradualism is no mere straw man, but rather continues to influence the work of top paleontologists.
Mark McMenamin and Dianna Schulte McMenamin argued that a formation of multiple ichthyosaur fossils (belonging to the genus Shonisaurus) placed together at Berlin–Ichthyosaur State Park may represent evidence of a gigantic cephalopod or Triassic kraken that killed the ichthyosaurs and intentionally arranged their bones in the unusual pattern seen at the site.
Opponents have challenged the theory as too far-fetched to be credible. PZ Myers believes that a much simpler explanation is that the rows of vertebral discs may be a result of the ichthyosaurs having fallen to one side or the other after death and rotting in that position, while Ryosuke Motani, a paleontologist at the University of California, Davis, has alternately proposed that the bones may have been moved together by ocean currents because of their circular shape. McMenamin has dismissed both of these concerns as not being in accord with either the sequence of bone placement or the hydrodynamics of the site. McMenamin was later quoted as saying: "When you consider that all other explanations for the Ichthyosaur death assemblage have failed, the plausibility goes up. It is currently the leading hypothesis, and none of the critics so far has proposed a fatal or even relatively significant objection."
Mark and Dianna McMenamin presented new evidence favoring the existence of the hypothesized Triassic kraken on October 31, 2013 at the Geological Society of America annual meeting in Denver, Colorado. Commentator David Fastovsky, speaking to the press after the talk, attempted to critique McMenamins' quantitative argument, but Fastovsky neglected to account for the fact that the vertebral array is both hydrodynamically unstable and could not have formed by passive collapse of a vertebral column because the vertebrae are out of order. McMenamin's probabilistic calculations assume currents strong enough to displace individual vertebrae, but the main argument holds even if no currents were present. Adolf Seilacher has noted that this ichthyosaur bone arrangement "has never been observed at other localities".McMenamin, Mark A. S.; McMenamin, Dianna Schulte. (Jan 1990). The Emergence of Animals: The Cambrian Breakthrough. Columbia University Press. ISBN 0-231-06646-5.
McMenamin, Mark A. S.; McMenamin, Dianna Schulte (1994). Hypersea: Life on the Land. Columbia University Press. ISBN 0-231-07530-8.
McMenamin, Mark A. S. (1996). Carthaginian Cartography: A Stylized Exergue Map. Meanma Press. ISBN 0-9651136-1-2.
McMenamin, Mark A. S. (1998). The Garden of Ediacara: Discovering the Earliest Complex Life. Columbia University Press.
McMenamin, Mark A. S. (Jun 2007). Science 101: Geology. Science 101. Collins. ISBN 0-06-089136-X.
McMenamin, Mark A. S. (2009). Paleotorus: The Laws of Morphogenetic Evolution. Meanma Press. ISBN 978-1-893882-18-8.