The league also saw the return of the Fresno Falcons to Selland Arena, after the team spent its first five seasons in the ECHL at the Save Mart Center on the campus of California State University, Fresno campus. However, this was short-lived, as Fresno joined the Augusta Lynx in suspending operations during the month of December.
On June 23, the ECHL announced the new divisional alignment of its 23 franchises. The league saw three teams vacate the South Division of the American Conference shrinking the division from nine to six teams and added a franchise to the Pacific Division of the National Conference increasing the division total from four teams to five. There will be thirteen teams in the American Conference, which stretches from New York south to Florida and from Mississippi east to New Jersey, and ten teams in the National Conference which stretches from Alaska south to Arizona.
On December 2, the Augusta Lynx suspended operations and voluntarily relinquished their membership to the league, in effect becoming the first team in the league's 21-year history to suspend midseason. Lynx owners stated that financial troubles and failed attempts to find additional investors were causes for the team to suspend operations. Dan Troutman, one of the team's owners, stated that he had asked the league to take over operations so the team could finish the season, but the move was voted down by the league's Board of Governors. The owners had also stated that attendance issues, in which Augusta has ranked no higher than 20th in the league the past three seasons, as the major reason for their financial problems as the team was successful in sponsorship issues.
On December 22, the Fresno Falcons became the second team in twenty days to cease operations, as the league's Board of Governors voted unanimously to terminate the franchise after Fresno's ownership notifying the league that they were unable to continue the membership for financial reasons. Fresno Hockey Club, LLC., the team's ownership group, cited "overwhelming financial issues due to declining attendance and dwindling corporate sponsorships" as reasons the team did not continue to operate for the 2008-09 season. This move comes less than a year after the team signed a 20-year lease with Selland Arena (starting with the 2008-09 season) and an agreement with the city of Fresno in which the city invested $5 million into upgrades for hockey at Selland Arena, as long as the team would not be sold or moved without the direct approval from the city. A clause in the agreement, stated that the city could take over the team as a government agency if owners were unable to continue operations; however, the option was declined after it was determined that the hockey club would finish the season $500,000 under expenses. City officials have expressed interest in bringing the franchise back as early as the 2009-10 season, although ECHL Commissioner was less enthusiastic stating that "a great deal of damage had been done" and that the league would give a new ownership "nine to ten months of lead time to create a solid foundation." At the time of their folding, the Falcons were in first place of the Pacific Division and had the fifth best record in the ECHL.
as of April 4, 2009 Note: GP = Games played; W = Wins; L= Loses; OTL = Overtime loses; SOL = Shootout loses; GF = Goals for; GA = Goals against; PTS = Points; PCT = Winning percentage; Green shade = Clinched playoff spot; Blue shade = Clinched division; Red shade = team is eliminated from playoffs; (z) = Clinched home-ice advantage
* Augusta folded on December 3, 2008. Fresno folded on December 22, 2008.
* Fresno's termination was announced on December 22, 2008, after ECHL All-Star voting had ended. As such, these players were voted as representatives of Fresno. Fallon's case is unique because he had moved to the American Conference. MacAulay joined head coach Matt Thomas at Stockton, in the National Conference
On June 23, the league announced its new playoff format for the 2008-09 season. The playoffs would feature a total of sixteen teams (eight from each conference) and four rounds of play. The top four finishers in each division will be seeded based on regular season point totals. The Division Semifinals will have the first seed meeting the fourth seed and the second seed meeting the third seed in a best-of-seven series. The winners of the Division Semifinals will advance to the Division Finals which is a best-of-seven series. The Division Finals winners will advance to the Conference Finals which is a best-of-seven series. The winner of the American Conference and the winner of the National Conference will meet in the Kelly Cup Finals, a best-of-seven game series. Home-ice advantage will be determined by regular season points. This format is similar to that used by the American Hockey League for the Calder Cup playoffs. 
At the Mid-Season Board of Governors Meeting in Reading, PA, during All-Star Game. two changes were announced for the playoff format due to Augusta and Fresno folding mid-season. In the National Conference, instead of the top four teams in each division making the playoffs, the top eight teams (of the nine in the conference) will make the playoffs; the fourth seed in the Pacific Division playoffs will be determined by the team with the better record between 4th place in the Pacific Division and 5th place in the Western Division. All seeding in the National Conference and in the American Conference's Southern Division will use percentage of points won because of an unbalanced number of games played caused by rescheduling (Points divided by Games, then divided by two).