IntelliJ IDEA can be used as a git mergetool. If you have merge conflicts, launching git mergetool will launch IntelliJ IDEA. Following configurations are required in ~/.gitconfig . Update the path to idea.exe accordingly.

Cygwin

[mergetool "ideamerge"]
     cmd = C:/Program\\ Files\\ \\(x86\\)/JetBrains/IntelliJ\\ IDEA\\ 13.1.3/bin/idea.exe merge `cygpath -wa $LOCAL` `cygpath -wa $REMOTE` `cygpath -wa $BASE` `cygpath -wa $MERGED`
[merge]
     tool = ideamerge

MSysGit

For MSysGit, we need to convert paths using our own script. Create ~/winpath.sh as

#! /bin/sh

function wpath {
    if [ -z "$1" ]; then
        echo "$@"
    else
        if [ -f "$1" ]; then
            local dir=$(dirname "$1")
            local fn=$(basename "$1")
            echo "$(cd "$dir"; echo "$(pwd -W)/$fn")" | sed 's|/|\\|g';
        else
            if [ -d "$1" ]; then
                echo "$(cd "$1"; pwd -W)" | sed 's|/|\\|g';
            else
                echo "$1" | sed 's|^/\(.\)/|\1:\\|g; s|/|\\|g';
            fi
        fi
    fi
}

wpath "$@"

[mergetool "ideamerge"]
cmd = "/c/Program\\ Files\\ \\(x86\\)/JetBrains/IntelliJ\\ IDEA\\ Community\\ Edition\\ 15.0.2/bin/idea.exe" merge `~/winpath.sh $LOCAL` `~/winpath.sh $REMOTE` `~/winpath.sh $BASE` `~/winpath.sh $MERGED`
[merge]
 tool = ideamerge