Plymouth chairman Sir Roy Gardner said: "Paul was fully aware that the board would review his position at the end of the season.
"We will now begin the process of seeking applications."
Mariner was handed responsibility of first-team duties at Home Park in December after Paul Sturrock was relieved of his managerial duties.
Mariner said: "I am disappointed that we could not produce the results we wanted last season.
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"I am a realist and understand why and how the board came to the conclusion they have done.
"I am committed to this club and want only to help it regain Championship status as soon as possible and build on that."
Plymouth ended the 2009/10 season second-bottom in the Championship, and facing their first season in League One for seven years.
Source: BBC Sport
Source: BBC Sport