The company's genesis was in December of 1991, where Genesis, participating in the government's Bus Installment Purchase Program, bought three midibuses to shuttle passengers between the Paskuhan Village in San Fernando, Pampanga and SM City North EDSA in Quezon City. Shortly after, in 1992, Genesis acquired franchises to operate regularly at the Mariveles-Pasay and Balanga-Pasay routes. Its network expanded to Mariveles-Dimasalang (Manila) and Baler-Pasay in 1993, becoming the first bus company to attempt (and succeed in) operating directly at the Baler-Pasay route

On its Bataan-NCR routes, Genesis had to contend with more established competitors: Panther Express, Viva Aladdin, and Philippine Rapid Transit, Inc. What set Genesis apart from the three companies was its pioneering innovations in operations: from the start, Genesis maximized usage of the North Diversion Road (now NLEX) by exiting at the San Fernando Exit, whereas its competitors used the traditional Tabang Exit-Manila North Road route; and where its competitors opted to pass thru Bataan town centers, Genesis took the path less travelled at the Roman Superhighway, cutting travel time to Balanga and Mariveles.

Genesis' rise to success was swift; by the turn of the century, they also had the Norzagaray-Baclaran via Taft NLEX and Balanga-Cubao routes to manage in addition to their old routes, as well as a few local routes in Central Luzon and towards Baguio City and La Union. It survived the 1997 Asian financial crises and its corresponding consequences, whereas its primary competitors in Bataan were left weakened. Using its power fleets of Nissan Diesel, Hino, and Mercedes-Benz among others, Genesis proceeded to conquer Central and Northern Luzon routes by increasing its number of franchises and authorized units.

Around 2002 or 2003, Genesis acquired Crow Transport Services, Inc., a major company in western Batangas and upland Cavite. Renamed the South Luzon Crown Transport, Inc., it became Genesis' first expansion to the south parts of Luzon, where it was challenged by the multitudes of small operators and even larger companies that operate in the relatively short routes in Cavite. Its major competition was Erjohn & Almark Transit Corp., which acquired SL Crown's assets from Genesis around 2008.

In 2010, Genesis made a major expansion by acquiring Saulog Transit, Inc. and its subsidiary, Dagupan Bus Company, Inc. Saulog and Dagupan, both large companies in Cavite and Pangasinan respectively, expanded the horizons of Genesis and marked its return to Cavite. Genesis integrated Saulog and Dagupan's operations into its own, making the three companies' garages, maintenance facilities, terminals, parts supply, and even manpower common among them.

Around that time as well, Genesis also started operating point-to-point deluxe and luxury services under the trade name Joybus. It was initially operated using Genesis' tourist bus fleets, offering trips to Baler and Baguio, popular tourist destinations especially during the summer. The Joybus service introduced "lazy-boy" seats in routes to Baguio and Baler, which they dubbed the "Executive Class" and later on introduced the "Premier Class" which added individual on-board entertainment for passengers in Baguio.

Starting in 2012 up to 2014, Genesis facilitated exchanges of franchises with Partas Transportation Company, Inc. Partas mainly operated in Ilocos Norte and La Union, but at that time also held an intra-regional franchise between Olongapo and San Jose, Nueva Ecija. Genesis sold its Baguio-Bolinao and La Union-NAIA franchises to Partas, who in turn sold its Baguio-NAIA and Olongapo-San Jose franchise to Genesis; the transaction solidified both companies' positions at their respective areas.

Around 2013, Genesis was granted the Clark DMIA-Trinoma route, becoming one of the few companies authorized to operate within the Clark Freeport Zone and up to the DMIA. Despite financial losses from operating to and from DMIA (due to a relative lack of passengers as compared to surrounding areas at Mabalacat and Angeles), Genesis held on to the route and even initiated services between DMIA and Baguio.

In 2015, Dagupan Bus was sold to the JAC Liner group. Genesis, however, retained possession of the Baguio-Cubao line of Dagupan. With this franchise, the company formed the North Genesis Bus Line, Inc. with the sole purpose of being Genesis' main arm in the route (by this time, all Genesis Transport buses from Baguio now operate from Pasay, Clark, and Mariveles).

Today, Genesis stands as one of the most influential and famous companies in Northern and Central Luzon. Its operations are divided among the following:

1. Genesis Transport Services, Inc. in Bataan-NCR, Mariveles-Baguio via San Fernando, San Fernando-San Jose via Cabanatuan, Baguio-Pasay (semi-deluxe with CR only) and P2P routes between Clark and Trinoma, Ortigas, and NAIA;

2. North Genesis Bus Line in Baguio-Cubao-Pasay (regular aircon);

3. Joybus, providing deluxe (2x1) and semi-deluxe (2x2) services between Baguio-NCR, Baler-NCR, and Baguio-Balanga via San Fernando;

4. Aurora Bus Line, between Cabanatuan and Baler, Maria Aurora, and Dipaculao in the province of Aurora; and

5. Saulog Transit Inc., operating in Ternate, Cavite City, and Olongapo.

Its major competitors include Bataan Transit in the Bataan line and Victory Liner in the Baguio line. In 2019, Solid North became another of Genesis' major competitor in Baguio when it beat Genesis in the bid for the exclusive Baguio-PITX route, and later introduced similar services offered by Joybus.

Genesis maintains a large variety of units (which, by their own estimate, is now about 400 in operation), which include units from (but not limited to): Yutong; Golden Dragon; Daewoo Bus; Volvo; Guilin Daewoo; and Zhongtong.